Variant report

Variant	rs16890301
Chromosome Location	chr6:37961583-37961584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37948324..37950868-chr6:37959290..37962178,2	MCF-7	breast:
2	chr6:37954058..37955830-chr6:37961204..37963273,2	K562	blood:
3	chr6:37961004..37963771-chr6:37970907..37973856,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000218521	Chromatin interaction

Extended variants
information (count: 192 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs10428769	0.80[ASN][1000 genomes]
rs10485030	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10498739	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10498740	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10947702	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10947704	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10947710	0.84[CHB][hapmap]
rs11750950	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs11751781	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11751927	0.89[ASN][1000 genomes]
rs11752521	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11753054	0.84[CHB][hapmap]
rs11755629	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11756713	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11756902	0.84[CHB][hapmap]
rs11757072	0.84[CHB][hapmap]
rs11758095	0.84[CHB][hapmap]
rs11759483	0.84[CHB][hapmap]
rs11759826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11964613	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs11964671	0.88[CEU][hapmap]
rs11969988	0.88[ASN][1000 genomes]
rs11970017	0.82[CEU][hapmap]
rs12660221	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs12660498	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs12660732	0.90[CHB][hapmap]
rs12660773	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12660919	0.89[ASN][1000 genomes]
rs12660922	0.81[ASN][1000 genomes]
rs12661073	0.90[CHB][hapmap]
rs12661109	0.81[ASN][1000 genomes]
rs12661129	0.81[CHB][hapmap]
rs12661378	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs12661480	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs12662305	0.89[CHB][hapmap]
rs12662426	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs12662823	0.81[ASN][1000 genomes]
rs12663427	0.90[CHB][hapmap]
rs12663957	0.81[ASN][1000 genomes]
rs12664091	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12664768	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12664900	0.84[CHB][hapmap]
rs13198459	1.00[CEU][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13203867	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13206035	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13207526	0.88[CEU][hapmap]
rs13210087	0.84[AFR][1000 genomes]
rs13210967	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs13212369	0.84[EUR][1000 genomes]
rs13217630	0.82[CEU][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs13219500	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16890175	0.80[CHD][hapmap]
rs16890177	0.90[CHB][hapmap]
rs16890181	0.90[CHB][hapmap]
rs16890194	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs16890215	0.90[CHB][hapmap]
rs16890247	0.90[CHB][hapmap]
rs16890267	0.89[ASN][1000 genomes]
rs16890298	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs16890299	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs16890305	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs16890307	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs16890309	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs16890341	0.83[CHB][hapmap]
rs16890362	0.90[CHB][hapmap]
rs16890365	0.82[ASW][hapmap];0.87[CEU][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs16890370	0.90[CHB][hapmap]
rs2055207	0.90[CHB][hapmap]
rs2055208	0.83[CHB][hapmap]
rs2064795	0.90[CHB][hapmap]
rs2145887	0.84[CHB][hapmap]
rs2273441	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2274090	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2274091	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2395689	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395692	0.84[CHB][hapmap]
rs2395693	0.84[CHB][hapmap]
rs2453882	0.88[CEU][hapmap]
rs2645096	0.88[CEU][hapmap]
rs2645098	0.88[CEU][hapmap]
rs2645104	0.88[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2645111	0.95[ASN][1000 genomes]
rs2645115	0.89[EUR][1000 genomes]
rs2645118	0.91[EUR][1000 genomes]
rs2645121	0.91[EUR][1000 genomes]
rs2645123	0.87[EUR][1000 genomes]
rs2645125	0.98[ASN][1000 genomes]
rs2645126	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2645130	0.90[ASN][1000 genomes]
rs28385568	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2842498	0.89[EUR][1000 genomes]
rs2842499	0.88[CEU][hapmap]
rs2842510	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2842511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2842512	0.91[ASN][1000 genomes]
rs2842514	0.88[CEU][hapmap]
rs2842516	0.88[CEU][hapmap]
rs2842521	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842524	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs33997846	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34038972	0.88[EUR][1000 genomes]
rs34123707	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34254045	0.89[ASN][1000 genomes]
rs34406273	0.88[EUR][1000 genomes]
rs34449592	0.86[AFR][1000 genomes]
rs34450348	0.92[ASN][1000 genomes]
rs34618835	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34634043	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34754573	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35051126	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35202194	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35465740	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35575717	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35597126	0.88[EUR][1000 genomes]
rs35772972	0.91[ASN][1000 genomes]
rs35815938	0.84[EUR][1000 genomes]
rs36069529	0.81[AFR][1000 genomes]
rs3800364	0.84[CHB][hapmap]
rs3844314	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3852216	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs4394213	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4524602	0.90[CHB][hapmap]
rs4711518	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs55786703	0.83[ASN][1000 genomes]
rs55943813	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56023538	0.92[ASN][1000 genomes]
rs56678832	0.82[EUR][1000 genomes]
rs57458792	0.85[ASN][1000 genomes]
rs57591988	0.81[ASN][1000 genomes]
rs58084785	0.84[ASN][1000 genomes]
rs58473303	0.81[ASN][1000 genomes]
rs59103990	0.81[ASN][1000 genomes]
rs59996041	0.84[ASN][1000 genomes]
rs60404082	0.81[ASN][1000 genomes]
rs60508820	0.81[ASN][1000 genomes]
rs61277916	0.83[ASN][1000 genomes]
rs6458032	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6458037	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906289	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6908761	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910837	0.88[CEU][hapmap]
rs6911481	0.88[CEU][hapmap]
rs6911716	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6916057	0.87[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs6917208	0.91[ASW][hapmap];0.87[CEU][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs6917736	0.86[AFR][1000 genomes]
rs6918802	1.00[CEU][hapmap]
rs6919884	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs6923132	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6923254	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6923665	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925563	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6940491	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs71569397	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs71569399	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71569402	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71571304	0.84[EUR][1000 genomes]
rs752110	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs7739801	0.83[CHB][hapmap]
rs7740636	0.88[EUR][1000 genomes]
rs7742226	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7745796	0.81[ASN][1000 genomes]
rs7746266	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7747996	0.89[ASN][1000 genomes]
rs7748312	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7748392	0.84[CHB][hapmap]
rs7756261	0.85[CHB][hapmap]
rs7757560	0.89[EUR][1000 genomes]
rs7759792	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7761561	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7764130	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7766767	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs7773419	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7775794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7776025	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs874095	0.90[CHB][hapmap]
rs876818	0.88[CHB][hapmap]
rs9296236	0.87[CEU][hapmap]
rs9470772	0.84[CHB][hapmap]
rs9470777	0.84[CHB][hapmap]
rs9470784	0.84[CHB][hapmap]
rs9470794	0.84[CHB][hapmap]
rs9470798	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37949800-37962000	Weak transcription	Small Intestine	intestine
2	chr6:37950000-37963600	Weak transcription	Spleen	Spleen
3	chr6:37953400-37962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:37953400-37962600	Weak transcription	Lung	lung
5	chr6:37953400-37965200	Weak transcription	Esophagus	oesophagus
6	chr6:37954200-37963000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:37955600-37963800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:37956200-37961800	Weak transcription	Fetal Brain Female	brain
9	chr6:37956200-37962000	Weak transcription	Fetal Stomach	stomach
10	chr6:37956200-37965400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:37956200-37978800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:37956600-37961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:37956600-37961800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:37956600-37962000	Weak transcription	Brain Angular Gyrus	brain
15	chr6:37956600-37962000	Weak transcription	Fetal Kidney	kidney
16	chr6:37956600-37967200	Weak transcription	Primary B cells from cord blood	blood
17	chr6:37956800-37961600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:37956800-37962000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:37957600-37961800	Weak transcription	Brain Germinal Matrix	brain
20	chr6:37957600-37962200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:37957600-37962400	Weak transcription	Pancreas	Pancrea
22	chr6:37957800-37961600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:37957800-37962200	Weak transcription	Fetal Brain Male	brain
24	chr6:37957800-37976400	Weak transcription	Aorta	Aorta
25	chr6:37958000-37961600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:37958000-37961800	Weak transcription	Fetal Lung	lung
27	chr6:37958800-37961600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:37958800-37961800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:37958800-37961800	Weak transcription	Brain Anterior Caudate	brain
30	chr6:37958800-37963200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:37959000-37961800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:37959000-37961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:37959000-37962000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:37959400-37961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:37959400-37962000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:37959400-37962000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:37959400-37962000	Weak transcription	Right Atrium	heart
38	chr6:37959400-37962600	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:37959400-37975600	Weak transcription	Left Ventricle	heart
40	chr6:37959600-37961600	Weak transcription	NHEK	skin
41	chr6:37959600-37961800	Weak transcription	HepG2	liver
42	chr6:37959600-37961800	Weak transcription	NH-A	brain
43	chr6:37959600-37962000	Weak transcription	Brain Substantia Nigra	brain
44	chr6:37959600-37962000	Weak transcription	HSMMtube	muscle
45	chr6:37959600-37962200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:37960000-37961600	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:37960000-37961800	Weak transcription	A549	lung
48	chr6:37960000-37961800	Weak transcription	NHDF-Ad	bronchial
49	chr6:37960200-37961600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:37960200-37962000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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