Variant report

Variant	rs2842521
Chromosome Location	chr6:37949168-37949169
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37948324..37950868-chr6:37959290..37962178,2	MCF-7	breast:

Extended variants
information (count: 155 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10428769	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10485030	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs10498739	0.85[CHB][hapmap]
rs10498740	0.85[CHB][hapmap]
rs10947702	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs10947704	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs10947710	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs11750950	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs11751781	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11751927	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11751962	0.83[AMR][1000 genomes]
rs11752521	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11752809	0.80[AMR][1000 genomes]
rs11752814	0.80[AMR][1000 genomes]
rs11752863	0.80[ASN][1000 genomes]
rs11753054	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs11753300	0.80[AMR][1000 genomes]
rs11755095	0.85[AMR][1000 genomes]
rs11755629	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11756713	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11756902	0.90[CHB][hapmap]
rs11757072	0.90[CHB][hapmap]
rs11757161	0.85[AMR][1000 genomes]
rs11757323	0.80[ASN][1000 genomes]
rs11758095	0.90[CHB][hapmap]
rs11759458	0.94[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs11759483	0.89[CHB][hapmap]
rs11759496	0.80[AMR][1000 genomes]
rs11759826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967129	0.85[AMR][1000 genomes]
rs11969988	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12660221	0.84[CHB][hapmap]
rs12660498	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs12660732	0.85[CHB][hapmap]
rs12660773	0.82[CHB][hapmap]
rs12660919	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12661073	0.85[CHB][hapmap]
rs12661378	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs12661480	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12661702	0.85[AMR][1000 genomes]
rs12662305	0.84[CHB][hapmap]
rs12662426	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs12663427	0.84[CHB][hapmap]
rs12664091	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12664768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12664900	0.89[CHB][hapmap]
rs13190751	0.80[AMR][1000 genomes]
rs13195545	0.85[AMR][1000 genomes]
rs13205214	0.93[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs13205311	0.85[AMR][1000 genomes]
rs13206035	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16890177	0.85[CHB][hapmap]
rs16890181	0.85[CHB][hapmap]
rs16890185	0.94[CEU][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs16890215	0.85[CHB][hapmap]
rs16890247	0.85[CHB][hapmap]
rs16890267	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890298	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs16890299	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs16890301	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16890305	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs16890307	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs16890309	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs16890341	0.84[CHB][hapmap]
rs16890362	0.85[CHB][hapmap]
rs16890370	0.85[CHB][hapmap]
rs1885324	0.84[CHB][hapmap]
rs2025431	0.85[AMR][1000 genomes]
rs2055207	0.85[CHB][hapmap]
rs2064795	0.85[CHB][hapmap]
rs2103950	0.80[AMR][1000 genomes]
rs2145887	0.90[CHB][hapmap]
rs2273441	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274090	0.84[CHB][hapmap]
rs2274091	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs2395689	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2395692	0.90[CHB][hapmap]
rs2395693	0.90[CHB][hapmap]
rs2645111	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645130	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842510	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842511	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2842512	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2842513	0.82[AFR][1000 genomes]
rs28740822	0.80[ASN][1000 genomes]
rs34254045	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34370874	0.80[ASN][1000 genomes]
rs34450348	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35051126	0.91[ASN][1000 genomes]
rs35122358	0.85[AMR][1000 genomes]
rs35216205	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35772972	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35849984	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3800364	0.89[CHB][hapmap]
rs3844314	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852216	0.84[CHB][hapmap]
rs4524602	0.85[CHB][hapmap]
rs55679841	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55786703	0.83[ASN][1000 genomes]
rs56023538	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56129320	0.83[AMR][1000 genomes]
rs56348433	0.80[ASN][1000 genomes]
rs56390138	0.80[ASN][1000 genomes]
rs57160603	0.80[ASN][1000 genomes]
rs57458792	0.84[ASN][1000 genomes]
rs57591988	0.81[ASN][1000 genomes]
rs57995712	0.80[ASN][1000 genomes]
rs58084785	0.82[ASN][1000 genomes]
rs58333612	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58611435	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59769374	0.80[ASN][1000 genomes]
rs59996041	0.84[ASN][1000 genomes]
rs61277916	0.82[ASN][1000 genomes]
rs61411293	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458032	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6903743	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6906289	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6908106	0.94[CEU][hapmap];0.90[YRI][hapmap]
rs6910715	0.94[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs6911716	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6936260	0.88[CEU][hapmap]
rs71569402	0.95[ASN][1000 genomes]
rs73421436	0.80[ASN][1000 genomes]
rs73421439	0.80[ASN][1000 genomes]
rs752110	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs7742226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs7745796	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7746266	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7747996	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7748312	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7748392	0.90[CHB][hapmap]
rs7759145	0.85[AMR][1000 genomes]
rs7759792	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761561	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs7762052	0.87[CEU][hapmap]
rs7764130	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs7773419	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7775794	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs874095	0.85[CHB][hapmap]
rs876818	0.94[CHB][hapmap]
rs9470772	0.90[CHB][hapmap]
rs9470777	0.90[CHB][hapmap]
rs9470784	0.90[CHB][hapmap]
rs9470794	0.89[CHB][hapmap]
rs9470798	0.89[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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37929400-37953200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:37934400-37949800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:37942400-37953200	Weak transcription	Esophagus	oesophagus
7	chr6:37942800-37949600	Weak transcription	Spleen	Spleen
8	chr6:37942800-37953600	Weak transcription	HepG2	liver
9	chr6:37942800-37956800	Weak transcription	Aorta	Aorta
10	chr6:37943000-37949800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:37943000-37951600	Weak transcription	NHDF-Ad	bronchial
12	chr6:37943000-37953000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:37943000-37955800	Weak transcription	Fetal Heart	heart
14	chr6:37943200-37951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:37943600-37951800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:37943600-37952400	Weak transcription	Gastric	stomach
17	chr6:37944800-37952000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:37945800-37949800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:37946200-37950400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:37946200-37953200	Weak transcription	GM12878-XiMat	blood
21	chr6:37946800-37950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:37946800-37955800	Weak transcription	Primary B cells from cord blood	blood
23	chr6:37947000-37949800	Enhancers	Psoas Muscle	Psoas
24	chr6:37947000-37950400	Enhancers	Duodenum Mucosa	Duodenum
25	chr6:37947200-37949200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr6:37947200-37949200	Enhancers	Right Ventricle	heart
27	chr6:37947200-37949400	Enhancers	Fetal Lung	lung
28	chr6:37947200-37949600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:37947200-37949800	Enhancers	Brain Anterior Caudate	brain
30	chr6:37947200-37949800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr6:37947200-37950000	Enhancers	Brain Hippocampus Middle	brain
32	chr6:37947200-37950000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:37947200-37950200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:37947200-37950400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr6:37947200-37950400	Enhancers	Brain Substantia Nigra	brain
36	chr6:37947200-37950600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:37947200-37951600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:37947400-37949200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:37947400-37949800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:37947400-37949800	Enhancers	Small Intestine	intestine
41	chr6:37947400-37950400	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:37947400-37950400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:37947400-37951800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:37947600-37949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:37947800-37949200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:37947800-37949200	Enhancers	Fetal Kidney	kidney
47	chr6:37947800-37949800	Enhancers	Adipose Nuclei	Adipose
48	chr6:37947800-37949800	Enhancers	Brain Angular Gyrus	brain
49	chr6:37947800-37950400	Enhancers	Primary B cells from peripheral blood	blood
50	chr6:37948000-37949600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links