Variant report

Variant	rs3852216
Chromosome Location	chr6:37874971-37874972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37874214..37875957-chr6:37876729..37879670,2	K562	blood:
2	chr6:37873838..37876151-chr6:37878592..37881455,2	K562	blood:
3	chr6:37873063..37875947-chr6:37943285..37945175,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL353597.1-10	chr6:37872575-37875797	NONHSAT112287

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10485030	0.85[CHB][hapmap]
rs10498739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10498740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10947702	0.85[CHB][hapmap]
rs10947704	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs10947710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11750950	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11751781	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs11751927	0.84[ASN][1000 genomes]
rs11752521	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs11752863	0.98[ASN][1000 genomes]
rs11753054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11755629	0.85[CHB][hapmap]
rs11756713	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11757072	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11757323	0.88[ASN][1000 genomes]
rs11759725	0.86[ASN][1000 genomes]
rs11759826	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11969988	0.82[ASN][1000 genomes]
rs12660221	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12660498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12660732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12660773	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12660919	0.83[ASN][1000 genomes]
rs12660922	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12661073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12661109	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12661378	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs12661480	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12662305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs12662426	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs12662823	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12663086	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12663427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12663957	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12664091	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs12664768	0.85[CHB][hapmap]
rs12664900	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs13206035	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs16890168	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs16890175	1.00[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap]
rs16890177	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16890181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16890215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16890247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16890267	0.84[ASN][1000 genomes]
rs16890298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16890299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16890301	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs16890305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890307	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16890309	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890341	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1885324	0.89[CHB][hapmap]
rs2055207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2055208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2064795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2273441	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs2274090	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2274091	0.85[CHB][hapmap]
rs2395689	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs2645130	0.82[ASN][1000 genomes]
rs2842510	0.85[CHB][hapmap];0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs2842511	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs2842512	0.82[ASN][1000 genomes]
rs2842521	0.84[CHB][hapmap]
rs28740822	0.88[ASN][1000 genomes]
rs34254045	0.83[ASN][1000 genomes]
rs34370874	0.88[ASN][1000 genomes]
rs34450348	0.83[ASN][1000 genomes]
rs35051126	0.84[ASN][1000 genomes]
rs35772972	0.82[ASN][1000 genomes]
rs3844314	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4524602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs55786703	0.91[ASN][1000 genomes]
rs56023538	0.83[ASN][1000 genomes]
rs56348433	0.88[ASN][1000 genomes]
rs56390138	0.88[ASN][1000 genomes]
rs57160603	0.88[ASN][1000 genomes]
rs57198506	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57276677	0.99[ASN][1000 genomes]
rs57458792	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57591988	0.93[ASN][1000 genomes]
rs57911756	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57995712	0.88[ASN][1000 genomes]
rs58084785	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58320470	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58473303	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58692659	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59036086	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59103990	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59649654	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59769374	0.88[ASN][1000 genomes]
rs59859268	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59996041	0.93[ASN][1000 genomes]
rs60141491	0.86[ASN][1000 genomes]
rs60284537	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60404082	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60508820	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60637081	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60883115	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61090283	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61108907	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61277916	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61332486	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61466900	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6458032	0.85[CHB][hapmap]
rs6906289	0.82[ASN][1000 genomes]
rs6911716	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs73421436	0.98[ASN][1000 genomes]
rs73421439	0.98[ASN][1000 genomes]
rs752110	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7739801	0.94[CHB][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7742226	0.84[CHB][hapmap]
rs7746266	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs7748312	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs7756261	0.85[CHB][hapmap]
rs7759792	0.85[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs7761561	0.80[CHB][hapmap]
rs7764130	0.85[CHB][hapmap]
rs7773419	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs7775794	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs9470772	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9470777	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37851000-37884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:37857600-37886000	Weak transcription	Esophagus	oesophagus
4	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
5	chr6:37858000-37877600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:37862000-37877000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:37862400-37877200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:37862400-37884000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:37862600-37882000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:37862800-37879000	Weak transcription	GM12878-XiMat	blood
11	chr6:37864600-37880800	Weak transcription	NHDF-Ad	bronchial
12	chr6:37865600-37879600	Weak transcription	Thymus	Thymus
13	chr6:37866000-37885600	Weak transcription	Hela-S3	cervix
14	chr6:37869400-37877000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:37870200-37877200	Weak transcription	Left Ventricle	heart
16	chr6:37871400-37879400	Weak transcription	K562	blood
17	chr6:37872000-37887600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
20	chr6:37872200-37883000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:37872200-37884000	Weak transcription	Adipose Nuclei	Adipose
22	chr6:37872200-37884600	Weak transcription	Fetal Kidney	kidney
23	chr6:37872400-37883000	Weak transcription	Brain Substantia Nigra	brain
24	chr6:37872600-37877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:37872600-37877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:37872600-37879600	Weak transcription	Psoas Muscle	Psoas
27	chr6:37872600-37885200	Weak transcription	HepG2	liver
28	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:37872800-37878400	Weak transcription	Fetal Heart	heart
30	chr6:37872800-37880600	Weak transcription	HMEC	breast
31	chr6:37872800-37880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:37873000-37882600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:37873200-37878400	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:37873200-37887400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:37873400-37877200	Weak transcription	Liver	Liver
36	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:37873600-37875200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:37873800-37876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:37874000-37878400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:37874200-37875800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:37874200-37884600	Weak transcription	A549	lung
43	chr6:37874400-37875400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr6:37874400-37876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:37874400-37876400	Weak transcription	Primary T cells from cord blood	blood
46	chr6:37874400-37877200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:37874400-37880800	Weak transcription	Osteobl	bone
48	chr6:37874400-37887600	Weak transcription	Spleen	Spleen
49	chr6:37874400-37888200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:37874600-37875000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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