Variant report

Variant	rs10863938
Chromosome Location	chr1:212262467-212262468
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	chr1:212260403..212263243-chr1:212265417..212267031,2	K562	blood:
2	chr1:212260044..212262870-chr1:212458652..212460803,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1017979	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10863933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1586660	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788128	1.00[AMR][1000 genomes]
rs2788129	1.00[AMR][1000 genomes]
rs2788130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs2788136	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788141	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2788142	1.00[CEU][hapmap]
rs2808380	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs2808382	0.81[GIH][hapmap]
rs2808383	1.00[CEU][hapmap]
rs2808384	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2808387	1.00[AMR][1000 genomes]
rs2808388	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2808390	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2970573	1.00[AMR][1000 genomes]
rs2970574	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2970575	1.00[AMR][1000 genomes]
rs2970576	1.00[CEU][hapmap]
rs2970585	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2970586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970588	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2970590	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970591	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970594	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970596	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2970597	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970598	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970600	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2970602	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2993524	1.00[CEU][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993525	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993526	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993527	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993530	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2993532	0.82[EUR][1000 genomes]
rs2993535	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2993536	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2993537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2993540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2993542	1.00[AMR][1000 genomes]
rs2993543	1.00[CEU][hapmap]
rs2993546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993548	1.00[AMR][1000 genomes]
rs2993549	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3009983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3009986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009990	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009992	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009993	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009995	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009996	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009998	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3009999	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3010000	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3010001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3010005	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3010008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs3010014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010015	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010017	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010018	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010019	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3010029	1.00[TSI][hapmap]
rs4309042	0.82[EUR][1000 genomes]
rs4397712	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4951437	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4951565	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6540717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6540718	1.00[AMR][1000 genomes]
rs6656826	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658972	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6672030	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6683980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689563	0.81[AFR][1000 genomes]
rs6704044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7532954	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545292	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs7551276	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:212229600-212266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212229800-212263000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:212229800-212266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:212230000-212265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:212233000-212266400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:212234000-212265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:212234000-212265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:212234200-212267400	Strong transcription	Dnd41	blood
10	chr1:212236000-212265200	Strong transcription	K562	blood
11	chr1:212237000-212266200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:212237200-212267000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:212237600-212266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:212241600-212264200	Weak transcription	Fetal Brain Female	brain
15	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:212244600-212267200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:212249400-212266000	Strong transcription	A549	lung
18	chr1:212253000-212270800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:212254800-212278000	Weak transcription	NHDF-Ad	bronchial
20	chr1:212256000-212266600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:212256000-212266800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:212256000-212271000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:212256400-212264800	Weak transcription	HepG2	liver
24	chr1:212256400-212265800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:212256400-212271200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:212256400-212278600	Weak transcription	NHLF	lung
27	chr1:212257200-212262800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:212259400-212264600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:212261000-212263400	Genic enhancers	Fetal Thymus	thymus
30	chr1:212261000-212263400	Enhancers	Right Atrium	heart
31	chr1:212261000-212264800	Enhancers	Fetal Heart	heart
32	chr1:212261000-212265200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:212261200-212263000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:212261200-212263400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:212261200-212263600	Enhancers	Primary T cells from cord blood	blood
36	chr1:212261200-212264400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:212261400-212262600	Enhancers	HUVEC	blood vessel
38	chr1:212261400-212263200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:212261600-212263000	Genic enhancers	GM12878-XiMat	blood
40	chr1:212261600-212263400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:212261800-212263000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:212261800-212263600	Enhancers	Primary B cells from cord blood	blood
43	chr1:212261800-212263600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:212261800-212264600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:212261800-212271800	Weak transcription	Spleen	Spleen
46	chr1:212262000-212263000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:212262000-212263000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:212262000-212263200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:212262000-212263200	Weak transcription	Fetal Intestine Large	intestine
50	chr1:212262000-212265200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links