Variant report

Variant	rs973889
Chromosome Location	chr2:172579954-172579955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:172579892-172582108	H1-neurons	neurons:	n/a	chr2:172581033-172581053 chr2:172581036-172581049 chr2:172580293-172580306

No.	Distal block	Cell Line	Cell type
1	chr2:172578420..172580000-chr2:172586848..172589301,2	MCF-7	breast:
2	chr2:172577655..172579971-chr2:172783366..172785140,2	K562	blood:
3	chr2:172578698..172580844-chr2:172604273..172606740,2	MCF-7	breast:
4	chr2:172577375..172580035-chr2:172580644..172583017,3	K562	blood:
5	chr2:172566910..172570582-chr2:172577373..172580278,3	K562	blood:

Variant related genes	Relation type
DYNC1I2	TF binding region
ENSG00000077380	Chromatin interaction
ENSG00000268821	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10166005	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10167419	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10174525	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10184866	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10194102	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10200608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201419	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10204502	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206062	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10207085	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10497374	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1113389	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11678984	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692132	0.85[YRI][hapmap]
rs11757	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11886820	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11897196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11904009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12053003	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12692973	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692974	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12692978	0.87[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13017585	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13018768	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13022113	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13419987	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13429113	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13429409	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474074	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1554166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973706	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2292815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357061	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2674484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678155	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs312916	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312919	0.91[AMR][1000 genomes]
rs312921	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs312924	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312925	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34358700	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34542126	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35379278	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35391289	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35549875	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35645520	0.82[AMR][1000 genomes]
rs35854280	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36057702	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770445	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770451	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770452	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795999	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667693	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4667694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4668407	0.81[EUR][1000 genomes]
rs4668412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668414	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433311	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433314	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66835971	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6705200	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6709156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710698	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67204065	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6721680	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722757	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724337	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6725388	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6727017	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs6738445	0.92[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6745143	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6754817	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6757773	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6758704	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6759575	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71013062	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7355523	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7355594	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7562356	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572215	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573003	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs7586207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7597387	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608403	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs908670	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs908671	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs973889	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs973889	AC068039.4	cis	lung	GTEx
rs973889	AC068039.4	cis	Esophagus Muscularis	GTEx
rs973889	AC068039.4	cis	Whole Blood	GTEx
rs973889	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs973889	AC068039.4	cis	Stomach	GTEx
rs973889	AC068039.4	cis	Esophagus Mucosa	GTEx
rs973889	AC068039.4	cis	Heart Left Ventricle	GTEx
rs973889	AC068039.4	cis	Muscle Skeletal	GTEx
rs973889	AC068039.4	cis	Nerve Tibial	GTEx
rs973889	AC068039.4	cis	Thyroid	GTEx
rs973889	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
2	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
3	chr2:172545000-172580800	Weak transcription	Gastric	stomach
4	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
7	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
8	chr2:172551600-172584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:172552200-172587600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:172554000-172580200	Weak transcription	Aorta	Aorta
11	chr2:172554400-172588000	Weak transcription	Esophagus	oesophagus
12	chr2:172554800-172580400	Weak transcription	K562	blood
13	chr2:172555000-172580200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:172557400-172584400	Weak transcription	Ovary	ovary
15	chr2:172558800-172583400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:172559000-172585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
18	chr2:172560400-172580800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:172561000-172583600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:172561200-172580200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:172561200-172587800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:172561400-172580200	Weak transcription	Brain Substantia Nigra	brain
23	chr2:172561400-172601800	Weak transcription	Fetal Heart	heart
24	chr2:172563200-172583000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:172563800-172583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:172564200-172610000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:172567000-172584200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:172569000-172584200	Weak transcription	Dnd41	blood
29	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:172569200-172582400	Weak transcription	A549	lung
31	chr2:172569200-172583400	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:172569200-172583600	Weak transcription	Hela-S3	cervix
33	chr2:172569400-172580400	Weak transcription	NHLF	lung
34	chr2:172569600-172580400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:172569800-172611400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:172570600-172580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:172571400-172597800	Strong transcription	HSMM	muscle
38	chr2:172571800-172594200	Strong transcription	HUVEC	blood vessel
39	chr2:172572000-172595400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:172572400-172580800	Weak transcription	NHEK	skin
41	chr2:172572400-172583200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:172573400-172581000	Weak transcription	Brain Angular Gyrus	brain
43	chr2:172573600-172584800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:172574800-172580800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:172574800-172587800	Weak transcription	Lung	lung
46	chr2:172575000-172580200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:172575200-172580200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:172575200-172580800	Weak transcription	Fetal Intestine Small	intestine
49	chr2:172575400-172580200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:172575400-172580800	Weak transcription	Left Ventricle	heart

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