Variant report

Variant	rs699165
Chromosome Location	chr3:136224697-136224698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135914471..135916410-chr3:136223365..136225971,2	MCF-7	breast:
2	chr3:136223066..136225762-chr3:136237795..136239369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1070232	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs10935186	0.93[JPT][hapmap]
rs1145106	0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap]
rs11715257	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs11717954	0.87[JPT][hapmap]
rs11919030	0.93[JPT][hapmap]
rs12489577	0.85[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs12630999	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs12635723	0.93[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap]
rs12637102	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs13068119	0.83[MEX][hapmap]
rs13433980	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs1394092	0.80[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs1484250	0.82[YRI][hapmap]
rs1711161	0.87[JPT][hapmap]
rs2062322	0.93[JPT][hapmap]
rs2655008	0.88[CEU][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs34602896	0.83[MEX][hapmap]
rs34967300	0.83[MEX][hapmap]
rs35375192	0.89[YRI][hapmap]
rs3856637	0.80[ASW][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs3932048	0.92[YRI][hapmap]
rs4408829	0.93[JPT][hapmap]
rs4521165	1.00[JPT][hapmap]
rs4678433	0.80[ASW][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs4678437	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4678438	0.93[ASW][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap]
rs483465	0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs58994059	0.82[ASN][1000 genomes]
rs595532	0.93[JPT][hapmap]
rs619605	0.93[JPT][hapmap]
rs6439642	0.81[YRI][hapmap]
rs6439649	1.00[JPT][hapmap]
rs650326	1.00[JPT][hapmap]
rs654237	0.93[JPT][hapmap]
rs655836	0.93[JPT][hapmap]
rs667920	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6782151	0.82[YRI][hapmap]
rs6791142	0.93[JPT][hapmap]
rs6791611	0.87[JPT][hapmap]
rs6794351	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs6804194	0.89[YRI][hapmap]
rs6808312	1.00[JPT][hapmap]
rs695983	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs696081	1.00[JPT][hapmap]
rs696516	0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap]
rs696517	0.83[MEX][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs711975	0.93[JPT][hapmap]
rs711976	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7432375	0.93[JPT][hapmap]
rs7612160	0.88[YRI][hapmap]
rs7618518	1.00[JPT][hapmap]
rs7618871	0.93[JPT][hapmap]
rs7620314	0.83[LWK][hapmap];0.80[YRI][hapmap]
rs7621025	0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs7644346	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs833752	0.80[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs900048	0.80[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9289511	0.89[CHB][hapmap]
rs940174	0.93[JPT][hapmap]
rs9812319	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs9820485	0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[ASN][1000 genomes]
rs9831321	0.82[YRI][hapmap]
rs9832056	0.89[CHB][hapmap]
rs9832813	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs9833207	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs9836231	0.93[JPT][hapmap]
rs9845762	0.93[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs9845950	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs9851986	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs9854084	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9856769	0.91[CHD][hapmap]
rs9868120	0.82[YRI][hapmap]
rs9869720	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs9883916	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs699165	PCCB	cis	lymphoblastoid	seeQTL
rs699165	MSL2	cis	cerebellum	SCAN
rs699165	NCK1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
3	chr3:136176600-136240000	Weak transcription	HMEC	breast
4	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
7	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:136193800-136231400	Weak transcription	NHLF	lung
12	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:136195200-136231000	Weak transcription	Osteobl	bone
14	chr3:136195400-136231400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:136195400-136232000	Weak transcription	Right Ventricle	heart
16	chr3:136195400-136241800	Weak transcription	NH-A	brain
17	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:136208400-136230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:136210200-136225800	Weak transcription	NHDF-Ad	bronchial
21	chr3:136210800-136229600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:136211600-136232000	Weak transcription	Fetal Kidney	kidney
23	chr3:136212200-136229200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:136212400-136231000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:136212400-136232000	Weak transcription	Aorta	Aorta
27	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:136212400-136249600	Weak transcription	Lung	lung
29	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
30	chr3:136213000-136231000	Weak transcription	Ovary	ovary
31	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
34	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:136213400-136231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:136214400-136238400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:136214600-136231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:136215000-136230000	Weak transcription	Fetal Lung	lung
43	chr3:136215600-136246200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:136216000-136224800	Strong transcription	Dnd41	blood
45	chr3:136218400-136227400	Weak transcription	Fetal Stomach	stomach
46	chr3:136218400-136227600	Weak transcription	Thymus	Thymus
47	chr3:136218400-136235000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:136218600-136235600	Weak transcription	HUVEC	blood vessel
49	chr3:136218800-136226400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:136219800-136231400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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