Variant report

Variant	rs4745646
Chromosome Location	chr9:71769323-71769324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71735309..71738649-chr9:71767224..71770432,5	MCF-7	breast:
2	chr9:71768614..71770999-chr9:71773509..71775018,2	K562	blood:
3	chr9:71758408..71761844-chr9:71769245..71771910,3	MCF-7	breast:
4	chr9:71768851..71770406-chr9:71807672..71810117,2	MCF-7	breast:
5	chr9:71735162..71738367-chr9:71767115..71770867,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10735653	0.85[MEX][hapmap]
rs10735655	0.87[CHB][hapmap]
rs10869992	0.87[CHB][hapmap]
rs10869993	0.87[CHB][hapmap]
rs10869994	0.87[CHB][hapmap]
rs10869997	0.86[CHB][hapmap]
rs11145460	0.80[CHB][hapmap]
rs11145501	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685829	0.83[ASN][1000 genomes]
rs17061543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17062126	0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs17062237	0.87[CHB][hapmap]
rs17062397	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2309422	0.87[CHB][hapmap]
rs2309425	0.87[CHB][hapmap]
rs2309426	0.93[CHB][hapmap]
rs2498428	0.81[JPT][hapmap]
rs2993817	0.85[MEX][hapmap]
rs2993820	0.87[CHB][hapmap]
rs3002379	0.85[CHB][hapmap]
rs3002382	0.87[CHB][hapmap]
rs4375066	0.87[CHB][hapmap]
rs4576478	0.87[CHB][hapmap]
rs4744837	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4745625	0.85[MEX][hapmap]
rs57733875	0.85[ASN][1000 genomes]
rs7024062	0.83[ASN][1000 genomes]
rs7850766	0.87[CHB][hapmap]
rs7854933	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7872806	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7875573	0.85[MEX][hapmap]
rs867346	0.93[CHB][hapmap]
rs884428	0.87[CHB][hapmap]
rs884429	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4745646	FXN	cis	parietal	SCAN
rs4745646	PIP5K1B	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71738000-71778200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:71738200-71770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:71745400-71770600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:71746400-71783200	Weak transcription	Small Intestine	intestine
5	chr9:71747000-71775600	Weak transcription	Hela-S3	cervix
6	chr9:71747200-71769800	Weak transcription	Placenta	Placenta
7	chr9:71749800-71770200	Weak transcription	Esophagus	oesophagus
8	chr9:71749800-71770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:71749800-71780600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:71752000-71780600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:71752000-71788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:71753200-71778800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:71755600-71788600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:71757600-71783800	Weak transcription	Stomach Mucosa	stomach
15	chr9:71762200-71774800	Strong transcription	Fetal Intestine Small	intestine
16	chr9:71762800-71769800	Weak transcription	NHEK	skin
17	chr9:71763000-71769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:71764400-71773800	Strong transcription	Fetal Intestine Large	intestine
19	chr9:71764600-71769800	Weak transcription	HMEC	breast
20	chr9:71764600-71770000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:71764600-71770600	Weak transcription	Adipose Nuclei	Adipose
22	chr9:71764600-71775400	Weak transcription	Pancreas	Pancrea
23	chr9:71764600-71783600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:71764600-71783800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:71764800-71769400	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:71764800-71770200	Weak transcription	Brain Substantia Nigra	brain
27	chr9:71764800-71770200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:71765000-71770200	Weak transcription	Fetal Lung	lung
29	chr9:71765000-71772600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:71765000-71779400	Weak transcription	Aorta	Aorta
31	chr9:71765000-71783000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:71765000-71787800	Weak transcription	Left Ventricle	heart
33	chr9:71765000-71788600	Weak transcription	Gastric	stomach
34	chr9:71765200-71778800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:71766200-71783800	Weak transcription	Thymus	Thymus
36	chr9:71766800-71771200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:71767000-71769400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:71767200-71769600	Enhancers	Stomach Smooth Muscle	stomach
39	chr9:71767400-71770200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:71767400-71772000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:71767400-71782800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:71767600-71769400	Strong transcription	Fetal Stomach	stomach
43	chr9:71767600-71769800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:71767600-71770200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:71767600-71770400	Weak transcription	Right Ventricle	heart
46	chr9:71767600-71770600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:71767600-71771200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:71767600-71776000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:71767600-71787800	Weak transcription	Fetal Heart	heart
50	chr9:71767600-71787800	Weak transcription	Rectal Smooth Muscle	rectum

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