Variant report

Variant	rs2670292
Chromosome Location	chr3:119369652-119369653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119367081..119370215-chr3:119370341..119373711,3	MCF-7	breast:
2	chr3:119367190..119369718-chr3:119370796..119372691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11914676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12487499	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.94[ASN][1000 genomes]
rs12490779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12492456	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525836	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203235	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985121	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2688629	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688634	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688635	0.88[LWK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs2692616	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35256565	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484809	0.85[JPT][hapmap]
rs524043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541479	0.83[AFR][1000 genomes]
rs571352	0.85[JPT][hapmap]
rs572119	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766563	0.89[CHB][hapmap]
rs67683909	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790938	0.86[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6794579	0.88[JPT][hapmap]
rs6803814	0.89[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7626940	0.89[CHB][hapmap]
rs8422	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816750	0.88[LWK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs9876919	0.95[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2670292	POPDC2	cis	lymphoblastoid	seeQTL
rs2670292	COX17	Cis_1M	lymphoblastoid	RTeQTL
rs2670292	COX17	cis	lymphoblastoid	seeQTL
rs2670292	POPDC2	cis	multi-tissue	Pritchard
rs2670292	RP11-190C22.1	cis	Heart Left Ventricle	GTEx
rs2670292	ILDR1	cis	cerebellum	SCAN

Chromatin state (count:72 , 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	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
13	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
19	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
20	chr3:119361400-119372600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:119362200-119371400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:119365200-119372200	Enhancers	Right Atrium	heart
29	chr3:119365200-119387400	Weak transcription	Liver	Liver
30	chr3:119367000-119371000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:119367000-119371000	Weak transcription	HSMM	muscle
32	chr3:119367200-119371000	Weak transcription	HSMMtube	muscle
33	chr3:119367200-119371200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:119367200-119375600	Weak transcription	GM12878-XiMat	blood
35	chr3:119367200-119378800	Weak transcription	Gastric	stomach
36	chr3:119367200-119381800	Weak transcription	Fetal Lung	lung
37	chr3:119367400-119370400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:119367400-119371200	Weak transcription	Spleen	Spleen
39	chr3:119367400-119371400	Weak transcription	Aorta	Aorta
40	chr3:119367400-119371400	Weak transcription	Fetal Stomach	stomach
41	chr3:119367400-119372800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:119367400-119375000	Weak transcription	Placenta	Placenta
43	chr3:119367400-119377800	Weak transcription	Fetal Intestine Small	intestine
44	chr3:119367400-119378000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:119367400-119378600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:119367400-119378800	Weak transcription	Pancreas	Pancrea
47	chr3:119367600-119371200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:119367600-119371400	Weak transcription	Lung	lung
49	chr3:119367600-119378200	Weak transcription	Fetal Intestine Large	intestine
50	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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