Variant report

Variant	rs2688629
Chromosome Location	chr3:119373315-119373316
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	chr3:119371437..119373754-chr3:119392688..119396112,3	K562	blood:
2	chr3:119371913..119374680-chr3:119377229..119379559,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11914676	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11923223	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12487499	0.92[ASN][1000 genomes]
rs12488460	0.92[ASN][1000 genomes]
rs12490779	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492456	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13062540	0.85[JPT][hapmap]
rs13065893	0.85[JPT][hapmap]
rs1403631	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1525836	0.92[ASN][1000 genomes]
rs16830115	0.95[ASN][1000 genomes]
rs16830291	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs17203235	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1797827	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880040	0.85[JPT][hapmap]
rs1985121	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2280578	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs2629395	0.85[JPT][hapmap]
rs2629409	0.85[JPT][hapmap]
rs2670292	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688634	0.94[ASN][1000 genomes]
rs2692616	0.89[ASN][1000 genomes]
rs2698283	0.99[ASN][1000 genomes]
rs34097211	0.95[ASN][1000 genomes]
rs34593263	0.92[ASN][1000 genomes]
rs34787881	0.95[ASN][1000 genomes]
rs35043554	0.92[ASN][1000 genomes]
rs35256565	0.95[ASN][1000 genomes]
rs3749416	0.85[JPT][hapmap]
rs3772134	0.85[JPT][hapmap]
rs4234662	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4327424	0.85[JPT][hapmap]
rs4629367	0.90[ASN][1000 genomes]
rs4687869	0.97[ASN][1000 genomes]
rs4688021	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4688023	0.85[JPT][hapmap]
rs4688024	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs484809	0.81[JPT][hapmap]
rs523476	0.85[JPT][hapmap]
rs524043	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs525916	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs540420	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs552244	0.85[JPT][hapmap]
rs571352	0.81[JPT][hapmap]
rs572119	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs575833	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs579196	0.95[ASN][1000 genomes]
rs6438542	0.85[JPT][hapmap]
rs6766563	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs67683909	0.97[ASN][1000 genomes]
rs6783324	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6789941	0.91[ASN][1000 genomes]
rs6790938	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792417	0.90[ASN][1000 genomes]
rs6794579	0.88[JPT][hapmap]
rs6803814	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs6807079	0.80[JPT][hapmap]
rs68150601	0.89[ASN][1000 genomes]
rs71325388	0.92[ASN][1000 genomes]
rs71325389	0.91[ASN][1000 genomes]
rs7613825	0.92[ASN][1000 genomes]
rs7626940	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs7633444	0.85[JPT][hapmap]
rs8422	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9876919	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2688629	COX17	Cis_1M	lymphoblastoid	RTeQTL
rs2688629	ILDR1	cis	cerebellum	SCAN
rs2688629	COX17	cis	lymphoblastoid	seeQTL
rs2688629	POPDC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
3	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
12	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
15	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:119365200-119387400	Weak transcription	Liver	Liver
23	chr3:119367200-119375600	Weak transcription	GM12878-XiMat	blood
24	chr3:119367200-119378800	Weak transcription	Gastric	stomach
25	chr3:119367200-119381800	Weak transcription	Fetal Lung	lung
26	chr3:119367400-119375000	Weak transcription	Placenta	Placenta
27	chr3:119367400-119377800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:119367400-119378000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:119367400-119378600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:119367400-119378800	Weak transcription	Pancreas	Pancrea
31	chr3:119367600-119378200	Weak transcription	Fetal Intestine Large	intestine
32	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
34	chr3:119367800-119378000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:119367800-119385400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:119367800-119386600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:119368000-119386000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:119368200-119388200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:119368800-119376400	Weak transcription	Primary T cells from cord blood	blood
41	chr3:119370600-119373600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:119370800-119374600	Transcr. at gene 5' and 3'	Fetal Heart	heart
43	chr3:119371400-119373400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:119371400-119373400	Strong transcription	Aorta	Aorta
45	chr3:119371600-119373400	Genic enhancers	Fetal Muscle Leg	muscle
46	chr3:119371600-119373800	Genic enhancers	Colon Smooth Muscle	Colon
47	chr3:119371600-119379200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:119371800-119378200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:119371800-119378800	Weak transcription	Spleen	Spleen
50	chr3:119372000-119373400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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