Variant report

Variant	rs16890341
Chromosome Location	chr6:38033254-38033255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38025431..38030854-chr6:38032452..38035354,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10498739	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10498740	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10947710	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11750950	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs11752799	0.86[ASN][1000 genomes]
rs11753054	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11753067	0.86[ASN][1000 genomes]
rs11753160	0.86[ASN][1000 genomes]
rs11755190	0.86[ASN][1000 genomes]
rs11755192	0.86[ASN][1000 genomes]
rs11756902	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11757072	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11757143	0.89[ASN][1000 genomes]
rs11757323	0.83[ASN][1000 genomes]
rs11758095	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11758747	0.89[ASN][1000 genomes]
rs11759483	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11759725	0.82[ASN][1000 genomes]
rs11759859	0.81[ASN][1000 genomes]
rs12660221	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12660498	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12660732	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12660773	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12661073	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12661109	0.84[ASN][1000 genomes]
rs12661129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12661480	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12662072	0.84[ASN][1000 genomes]
rs12662305	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12662543	0.86[ASN][1000 genomes]
rs12662823	0.84[ASN][1000 genomes]
rs12662940	0.86[ASN][1000 genomes]
rs12663086	0.83[ASN][1000 genomes]
rs12663207	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12663406	0.85[ASN][1000 genomes]
rs12663427	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12663450	0.85[ASN][1000 genomes]
rs12663957	0.84[ASN][1000 genomes]
rs12664900	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12665229	0.87[ASN][1000 genomes]
rs16890215	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890247	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890298	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890299	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16890301	0.83[CHB][hapmap]
rs16890305	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16890307	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16890309	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16890362	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16890370	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1885324	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1885326	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2055207	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2055208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2073021	0.86[ASN][1000 genomes]
rs2145886	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2145887	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2145888	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2281264	0.87[ASN][1000 genomes]
rs2281265	0.86[ASN][1000 genomes]
rs2395689	0.83[CHB][hapmap]
rs2395692	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2395693	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2842511	0.84[CHB][hapmap]
rs2842521	0.84[CHB][hapmap]
rs28740822	0.83[ASN][1000 genomes]
rs34370874	0.83[ASN][1000 genomes]
rs3800364	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3852216	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4524602	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55786703	0.80[ASN][1000 genomes]
rs56247028	0.86[ASN][1000 genomes]
rs56348433	0.83[ASN][1000 genomes]
rs56390138	0.83[ASN][1000 genomes]
rs56688119	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56739079	0.87[ASN][1000 genomes]
rs56914148	0.89[ASN][1000 genomes]
rs56957219	0.87[ASN][1000 genomes]
rs57142729	0.99[ASN][1000 genomes]
rs57160603	0.83[ASN][1000 genomes]
rs57208246	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57236731	0.87[ASN][1000 genomes]
rs57405566	0.86[ASN][1000 genomes]
rs57409051	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57525562	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57537146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57630694	0.87[ASN][1000 genomes]
rs57812773	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57995712	0.83[ASN][1000 genomes]
rs58084785	0.81[ASN][1000 genomes]
rs58204078	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58332635	0.99[ASN][1000 genomes]
rs58397443	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58473303	0.84[ASN][1000 genomes]
rs59074919	0.87[ASN][1000 genomes]
rs59170481	0.87[ASN][1000 genomes]
rs59219746	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59350040	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59430914	0.82[ASN][1000 genomes]
rs59578279	0.89[ASN][1000 genomes]
rs59684841	0.86[ASN][1000 genomes]
rs59769374	0.83[ASN][1000 genomes]
rs60075988	0.87[ASN][1000 genomes]
rs60404082	0.84[ASN][1000 genomes]
rs60425175	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60508820	0.84[ASN][1000 genomes]
rs60883115	0.82[ASN][1000 genomes]
rs60986358	0.86[ASN][1000 genomes]
rs61146875	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61172238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73419927	0.97[ASN][1000 genomes]
rs73419930	0.98[ASN][1000 genomes]
rs73419955	0.89[ASN][1000 genomes]
rs73419996	0.89[ASN][1000 genomes]
rs73734319	0.87[ASN][1000 genomes]
rs73734323	0.87[ASN][1000 genomes]
rs752110	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7739801	0.94[CHB][hapmap]
rs7745340	0.85[ASN][1000 genomes]
rs7746266	0.84[CHB][hapmap]
rs7748392	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7748913	0.82[ASN][1000 genomes]
rs7760452	0.86[ASN][1000 genomes]
rs874095	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs876818	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9462389	0.86[ASN][1000 genomes]
rs9462393	0.86[ASN][1000 genomes]
rs9462394	0.86[ASN][1000 genomes]
rs9462395	0.86[ASN][1000 genomes]
rs9462396	0.85[ASN][1000 genomes]
rs9462397	0.87[ASN][1000 genomes]
rs9462398	0.86[ASN][1000 genomes]
rs9470772	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9470777	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9470784	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9470794	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9470796	0.86[ASN][1000 genomes]
rs9470798	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9470802	0.86[ASN][1000 genomes]

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	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
3	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
4	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
5	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
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38020400-38046200	Weak transcription	Stomach Mucosa	stomach
3	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:38023200-38052800	Weak transcription	Gastric	stomach
5	chr6:38024400-38040000	Weak transcription	Fetal Heart	heart
6	chr6:38024600-38033800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:38024600-38035200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:38024600-38041800	Weak transcription	Fetal Brain Male	brain
9	chr6:38024600-38045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:38026000-38035200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:38026000-38047600	Weak transcription	Hela-S3	cervix
12	chr6:38026200-38053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:38028200-38034200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:38028400-38036800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr6:38029000-38033400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:38029000-38033600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr6:38029200-38033600	Strong transcription	Placenta	Placenta
18	chr6:38029200-38034000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:38029400-38033400	Strong transcription	NH-A	brain
20	chr6:38029400-38033800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:38029400-38034000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:38029400-38034000	Strong transcription	HepG2	liver
23	chr6:38029400-38034200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr6:38029400-38034400	Strong transcription	Primary T cells from cord blood	blood
25	chr6:38029600-38035200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:38030000-38034800	Weak transcription	Ovary	ovary
27	chr6:38030000-38035200	Weak transcription	Small Intestine	intestine
28	chr6:38030400-38037800	Weak transcription	Pancreas	Pancrea
29	chr6:38030600-38035600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:38030600-38035800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:38030800-38036000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:38030800-38036600	Weak transcription	Fetal Intestine Small	intestine
33	chr6:38030800-38041600	Weak transcription	HMEC	breast
34	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:38031000-38034800	Weak transcription	Psoas Muscle	Psoas
36	chr6:38031400-38034400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:38031400-38035200	Weak transcription	Brain Anterior Caudate	brain
38	chr6:38031400-38035600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:38031400-38039400	Weak transcription	K562	blood
40	chr6:38031400-38042400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:38031400-38045000	Weak transcription	Aorta	Aorta
42	chr6:38031400-38052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:38031600-38034000	Weak transcription	Esophagus	oesophagus
44	chr6:38031600-38034800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:38031600-38035200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:38031600-38035200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:38031600-38035600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:38031600-38035800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:38031600-38037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:38031600-38039800	Weak transcription	Brain Inferior Temporal Lobe	brain

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