Variant report

Variant	rs6658972
Chromosome Location	chr1:212251103-212251104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212250997..212252967-chr1:212253483..212255287,2	MCF-7	breast:
2	chr1:212183715..212186180-chr1:212250806..212253647,2	K562	blood:
3	chr1:212220183..212221009-chr1:212251102..212251717,4	MCF-7	breast:
4	chr1:212251050..212251666-chr1:212311724..212312461,3	MCF-7	breast:
5	chr1:212247974..212251489-chr1:212456327..212461743,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143476	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000143493	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1017979	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs10863933	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10863934	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10863938	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10863940	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2788128	1.00[AMR][1000 genomes]
rs2788129	1.00[AMR][1000 genomes]
rs2788130	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788131	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788134	1.00[AMR][1000 genomes]
rs2788135	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2788136	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788137	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788141	1.00[CEU][hapmap]
rs2788142	1.00[CEU][hapmap]
rs2808380	1.00[YRI][hapmap]
rs2808383	1.00[CEU][hapmap]
rs2808384	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2808387	1.00[AMR][1000 genomes]
rs2808390	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2970573	1.00[AMR][1000 genomes]
rs2970574	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2970575	1.00[AMR][1000 genomes]
rs2970576	1.00[CEU][hapmap]
rs2970585	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2970586	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970588	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2970590	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970591	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970594	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970596	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2970597	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970600	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2970602	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2993524	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993525	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993526	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993527	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993530	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2993532	0.81[EUR][1000 genomes]
rs2993536	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2993537	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2993540	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2993542	1.00[AMR][1000 genomes]
rs2993543	1.00[CEU][hapmap]
rs2993546	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2993548	1.00[AMR][1000 genomes]
rs2993549	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3009983	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3009986	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009990	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009992	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009993	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009994	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009995	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009996	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009998	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3009999	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3010000	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3010001	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3010005	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs3010008	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs3010014	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010015	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010017	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010018	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010019	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010020	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010021	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3010022	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4397712	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs4951437	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4951565	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6540717	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6540718	1.00[AMR][1000 genomes]
rs6656826	1.00[CEU][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6672030	1.00[CEU][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6683980	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6704044	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7551276	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212209600-212253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:212229600-212255400	Weak transcription	NHLF	lung
4	chr1:212229600-212266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:212229800-212255800	Weak transcription	Thymus	Thymus
6	chr1:212229800-212261000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:212229800-212261200	Weak transcription	Fetal Stomach	stomach
8	chr1:212229800-212261400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:212229800-212263000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:212229800-212266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:212230000-212255200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:212230000-212255400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:212230000-212261200	Weak transcription	Osteobl	bone
14	chr1:212230000-212265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:212230800-212261800	Weak transcription	Primary B cells from cord blood	blood
16	chr1:212231000-212255400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:212231400-212253000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:212231400-212261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:212233000-212255000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:212233000-212266400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212234000-212265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:212234000-212265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:212234200-212267400	Strong transcription	Dnd41	blood
24	chr1:212236000-212265200	Strong transcription	K562	blood
25	chr1:212237000-212261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:212237000-212266200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:212237200-212267000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:212237600-212260800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:212237600-212266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:212237800-212262000	Strong transcription	Hela-S3	cervix
31	chr1:212238000-212251600	Weak transcription	NHDF-Ad	bronchial
32	chr1:212238000-212251800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:212238200-212261200	Weak transcription	NH-A	brain
34	chr1:212238400-212253200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:212239000-212253200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:212240600-212253400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:212240600-212253400	Weak transcription	HepG2	liver
38	chr1:212241600-212264200	Weak transcription	Fetal Brain Female	brain
39	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:212242000-212261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:212243400-212254600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:212244200-212253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:212244200-212254200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:212244400-212253400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:212244600-212267200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:212245000-212255600	Strong transcription	GM12878-XiMat	blood
47	chr1:212245200-212254000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:212245800-212252400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:212245800-212255000	Weak transcription	Fetal Lung	lung
50	chr1:212246000-212253200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links