Variant report

Variant	rs629412
Chromosome Location	chr1:47120673-47120674
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	chr1:47118515..47120861-chr1:47128055..47129581,2	MCF-7	breast:
2	chr1:47120180..47123031-chr1:47124128..47126254,2	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10890410	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs10890414	0.92[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11211347	0.80[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12562113	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12566278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568734	0.92[ASN][1000 genomes]
rs1258010	1.00[TSI][hapmap]
rs1258022	1.00[TSI][hapmap]
rs1258055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258058	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258063	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1258064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258068	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1268714	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1745376	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1933932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146560	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439442	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476153	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476156	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476159	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486162	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3011290	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766221	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766223	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56771521	0.92[ASN][1000 genomes]
rs57495753	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs583649	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58678760	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59479990	0.92[ASN][1000 genomes]
rs596794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597221	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs611919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636424	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648822	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655369	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657166	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs673134	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675731	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs678466	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs683585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs689300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs723333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs724309	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72900715	0.92[ASN][1000 genomes]
rs736188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
6	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
9	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
10	chr1:47108200-47123400	Weak transcription	K562	blood
11	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
12	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
13	chr1:47109600-47123400	Weak transcription	NH-A	brain
14	chr1:47109600-47132600	Weak transcription	HMEC	breast
15	chr1:47109800-47123200	Weak transcription	HepG2	liver
16	chr1:47112200-47125600	Strong transcription	Liver	Liver
17	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:47112800-47125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:47112800-47125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:47113000-47124400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr1:47113600-47121800	Weak transcription	NHEK	skin
22	chr1:47114600-47124600	Strong transcription	Fetal Thymus	thymus
23	chr1:47115000-47125200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:47115000-47125400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:47115400-47124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:47115800-47121600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:47115800-47121800	Weak transcription	Psoas Muscle	Psoas
29	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
30	chr1:47116000-47121400	Weak transcription	Dnd41	blood
31	chr1:47116000-47121600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:47116000-47121800	Weak transcription	Right Ventricle	heart
33	chr1:47116000-47123800	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
35	chr1:47116000-47130000	Weak transcription	Lung	lung
36	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
37	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
38	chr1:47116200-47121600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:47116400-47120800	Weak transcription	Brain Germinal Matrix	brain
40	chr1:47116400-47121800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:47116600-47122200	Weak transcription	HSMMtube	muscle
42	chr1:47116600-47123200	Weak transcription	HSMM	muscle
43	chr1:47116600-47130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:47117000-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:47117400-47121600	Strong transcription	Adipose Nuclei	Adipose
47	chr1:47117600-47124000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:47117600-47124400	Strong transcription	Brain Angular Gyrus	brain
49	chr1:47117600-47125200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:47117600-47125400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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