Variant report

Variant	rs3002379
Chromosome Location	chr9:71802812-71802813
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71735548..71738179-chr9:71802464..71805527,4	MCF-7	breast:
2	chr9:71793437..71796575-chr9:71800849..71803990,3	MCF-7	breast:
3	chr9:71800754..71805797-chr9:71805912..71810495,5	K562	blood:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10125494	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10217168	0.82[JPT][hapmap]
rs10735655	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781440	0.82[JPT][hapmap]
rs10781456	0.82[JPT][hapmap]
rs10781479	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10869961	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10869975	0.80[CHB][hapmap]
rs10869992	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10869993	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10869994	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10869997	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10870006	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10870012	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10870015	0.94[ASN][1000 genomes]
rs10870017	0.94[ASN][1000 genomes]
rs11145460	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs11145627	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11145648	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11145688	0.93[ASN][1000 genomes]
rs12056979	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1339546	0.82[JPT][hapmap]
rs1416738	0.81[JPT][hapmap]
rs1538584	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs17062237	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17062397	0.85[CHB][hapmap]
rs2309422	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2309424	0.82[JPT][hapmap]
rs2309425	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309426	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2309427	0.91[ASN][1000 genomes]
rs2486449	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2486451	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2486452	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2498436	0.94[ASN][1000 genomes]
rs2993818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2993819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993820	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002380	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002382	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750549	0.91[ASN][1000 genomes]
rs3927676	0.93[ASN][1000 genomes]
rs4076287	0.82[JPT][hapmap]
rs4338173	0.93[ASN][1000 genomes]
rs4375066	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4576478	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592105	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs4745646	0.85[CHB][hapmap]
rs4745701	0.82[JPT][hapmap]
rs55641500	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56226859	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs56312702	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58264616	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs60785288	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs61074083	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62567148	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6560618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560627	0.91[ASN][1000 genomes]
rs7020869	0.94[ASN][1000 genomes]
rs7038854	0.94[ASN][1000 genomes]
rs7041781	0.91[ASN][1000 genomes]
rs7043149	0.82[JPT][hapmap]
rs7045103	0.92[ASN][1000 genomes]
rs7048648	0.91[ASN][1000 genomes]
rs7350225	0.93[ASN][1000 genomes]
rs7467352	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs7850766	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861292	0.93[ASN][1000 genomes]
rs7862404	0.84[CHB][hapmap]
rs7864775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865373	0.82[JPT][hapmap]
rs7873004	0.91[ASN][1000 genomes]
rs7874888	0.87[ASN][1000 genomes]
rs867346	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs884428	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs884429	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9410783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9411195	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9411200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
rs3002379	TJP2	cis	Whole Blood	GTEx
rs3002379	TJP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71791200-71807600	Weak transcription	Psoas Muscle	Psoas
4	chr9:71791400-71804400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr9:71792400-71808800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:71793600-71805600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:71794000-71806000	Weak transcription	Primary T cells from cord blood	blood
8	chr9:71795600-71814400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:71795800-71804200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:71795800-71806400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:71796000-71805600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:71797000-71805800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:71797000-71814600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:71797200-71804000	Weak transcription	Lung	lung
15	chr9:71797200-71805800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:71797200-71832000	Weak transcription	Esophagus	oesophagus
17	chr9:71798400-71807400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:71799200-71804600	Enhancers	Placenta	Placenta
19	chr9:71799600-71808400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:71800600-71806600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:71800800-71803200	Enhancers	HMEC	breast
22	chr9:71800800-71803400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:71801000-71803000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:71801000-71803000	Enhancers	Osteobl	bone
25	chr9:71801000-71803400	Enhancers	HUVEC	blood vessel
26	chr9:71801000-71803400	Genic enhancers	NHEK	skin
27	chr9:71801000-71803600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:71801000-71804000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr9:71801000-71804600	Enhancers	Stomach Mucosa	stomach
30	chr9:71801000-71811800	Enhancers	Liver	Liver
31	chr9:71801200-71803000	Enhancers	Adipose Nuclei	Adipose
32	chr9:71801200-71803200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:71801200-71803200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:71801200-71803200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr9:71801200-71803200	Enhancers	Fetal Intestine Small	intestine
36	chr9:71801200-71803200	Enhancers	Fetal Stomach	stomach
37	chr9:71801200-71803400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:71801400-71803000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:71801400-71803000	Enhancers	HSMM	muscle
40	chr9:71801400-71805200	Enhancers	GM12878-XiMat	blood
41	chr9:71801600-71809600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:71801800-71803000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:71801800-71803200	Enhancers	Rectal Smooth Muscle	rectum
44	chr9:71801800-71804600	Enhancers	Brain Substantia Nigra	brain
45	chr9:71802000-71803000	Weak transcription	Fetal Intestine Large	intestine
46	chr9:71802000-71803400	Enhancers	Aorta	Aorta
47	chr9:71802200-71803000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr9:71802200-71803400	Genic enhancers	HepG2	liver
49	chr9:71802200-71804000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:71802200-71808000	Weak transcription	Fetal Muscle Leg	muscle

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