Variant report

Variant	rs7871596
Chromosome Location	chr9:71657397-71657398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:71657250-71657449	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:71655778..71657735-chr9:71659824..71661960,2	K562	blood:
2	chr9:71655862..71658846-chr9:71661896..71664645,2	MCF-7	breast:
3	chr9:71651712..71654573-chr9:71656499..71659593,3	K562	blood:

Variant related genes	Relation type
FXN	TF binding region
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10126006	0.91[CHB][hapmap];0.84[TSI][hapmap]
rs10781379	0.82[CHB][hapmap]
rs10890	0.82[CHB][hapmap]
rs11145043	0.82[CHB][hapmap]
rs1411675	0.82[CHB][hapmap]
rs1411676	0.82[CHB][hapmap]
rs1815427	0.82[ASN][1000 genomes]
rs1984004	0.81[CHB][hapmap]
rs2309393	0.82[CHB][hapmap]
rs2309394	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481600	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2498427	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2498430	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs2498431	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2498433	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2498434	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2871218	0.81[ASN][1000 genomes]
rs3763608	0.83[MEX][hapmap]
rs3793456	0.91[CHB][hapmap]
rs3793457	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3793459	0.85[ASN][1000 genomes]
rs3793460	0.84[ASN][1000 genomes]
rs3793461	0.82[CHB][hapmap]
rs3793465	0.81[CHB][hapmap]
rs3793466	0.82[CHB][hapmap]
rs3793467	0.82[CHB][hapmap]
rs3829062	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829064	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs4744807	0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744808	0.82[CHB][hapmap]
rs4745553	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745577	0.82[CHB][hapmap]
rs4745580	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4745581	0.82[CHB][hapmap]
rs61290674	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7025834	0.81[ASN][1000 genomes]
rs7047274	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849347	0.82[CHB][hapmap]
rs7855905	0.82[CHB][hapmap]
rs7861997	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7865353	0.89[AMR][1000 genomes]
rs7870295	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7875659	0.82[CHB][hapmap]
rs7875693	0.82[CHB][hapmap]
rs9314854	0.82[CHB][hapmap]
rs9411170	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9411171	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs944348	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
19	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
23	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
25	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
26	nsv466398	chr9:71612891-71671116	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv614551	chr9:71612891-71671116	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
29	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
30	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7871596	TJP2	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71651400-71663800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:71651600-71661800	Weak transcription	Fetal Brain Female	brain
3	chr9:71651800-71658800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:71651800-71659400	Weak transcription	Gastric	stomach
5	chr9:71651800-71661400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:71651800-71661600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:71651800-71680600	Weak transcription	HSMMtube	muscle
8	chr9:71652000-71658200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:71652000-71658800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr9:71652000-71659000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:71652000-71659000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:71652000-71659000	Weak transcription	Fetal Heart	heart
13	chr9:71652000-71659000	Weak transcription	Fetal Lung	lung
14	chr9:71652000-71659200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:71652000-71659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:71652000-71659200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:71652000-71659200	Weak transcription	Colonic Mucosa	Colon
18	chr9:71652000-71659200	Weak transcription	Pancreas	Pancrea
19	chr9:71652000-71659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:71652000-71659400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:71652000-71659400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:71652000-71659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:71652000-71659400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:71652000-71659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:71652000-71659400	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:71652000-71659400	Weak transcription	Lung	lung
27	chr9:71652000-71659400	Weak transcription	Right Ventricle	heart
28	chr9:71652000-71659400	Weak transcription	Hela-S3	cervix
29	chr9:71652000-71659600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:71652000-71659600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:71652000-71659600	Weak transcription	GM12878-XiMat	blood
32	chr9:71652000-71659600	Weak transcription	NH-A	brain
33	chr9:71652000-71660600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:71652000-71661000	Weak transcription	HSMM	muscle
35	chr9:71652000-71661400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:71652000-71661400	Weak transcription	Esophagus	oesophagus
37	chr9:71652000-71661600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr9:71652000-71661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:71652000-71661600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:71652000-71661600	Weak transcription	Fetal Intestine Large	intestine
41	chr9:71652000-71661800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:71652000-71661800	Weak transcription	Brain Anterior Caudate	brain
43	chr9:71652000-71661800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:71652000-71661800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:71652000-71661800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr9:71652000-71661800	Weak transcription	NHEK	skin
47	chr9:71652000-71662000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:71652000-71663000	Weak transcription	Dnd41	blood
49	chr9:71652000-71663600	Weak transcription	Brain Substantia Nigra	brain
50	chr9:71652000-71663600	Weak transcription	A549	lung

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