Variant report

Variant	rs16890194
Chromosome Location	chr6:37813283-37813284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37786385..37788303-chr6:37812981..37815749,2	MCF-7	breast:
2	chr6:37810232..37811886-chr6:37811950..37813502,2	K562	blood:
3	chr6:37811967..37814483-chr6:37816541..37818397,2	MCF-7	breast:
4	chr6:37792689..37794670-chr6:37813133..37814800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11752809	0.87[ASN][1000 genomes]
rs11752814	0.87[ASN][1000 genomes]
rs11753300	0.87[ASN][1000 genomes]
rs11759458	1.00[JPT][hapmap];0.80[MKK][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs11964613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968604	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970145	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190751	0.87[ASN][1000 genomes]
rs13198459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13200310	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13203867	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13205214	1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs13207526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210967	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13211881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218158	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890185	1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs16890301	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs2103950	0.96[ASN][1000 genomes]
rs2395689	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs2453882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2645115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2645118	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2645121	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2645123	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2645126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2842498	1.00[AMR][1000 genomes]
rs2842499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842506	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842511	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2842512	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842513	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34011349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054102	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34611895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745343	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35248825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35330991	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35379375	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35609407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35653300	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35849984	0.84[ASN][1000 genomes]
rs35953900	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35955196	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36069529	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4394213	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56391784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458037	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6908106	1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs6908761	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6910715	0.82[JPT][hapmap]
rs6910837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6911481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6912250	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6918802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919884	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6923132	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6923254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6925563	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933547	1.00[YRI][hapmap]
rs6936260	0.82[JPT][hapmap]
rs6940491	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71569395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7742379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7747538	0.84[AMR][1000 genomes]
rs7750445	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7757560	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7760770	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762052	0.82[JPT][hapmap]
rs7776025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:37793800-37813600	Weak transcription	NH-A	brain
5	chr6:37794000-37819800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:37795000-37813800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:37795000-37825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:37795800-37813400	Weak transcription	HSMMtube	muscle
9	chr6:37796000-37813800	Weak transcription	NHDF-Ad	bronchial
10	chr6:37796000-37815600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:37796000-37828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:37796000-37830600	Weak transcription	Hela-S3	cervix
13	chr6:37798400-37815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:37798400-37815800	Weak transcription	Fetal Heart	heart
15	chr6:37799400-37817400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:37799600-37813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:37799600-37825800	Weak transcription	Esophagus	oesophagus
18	chr6:37799800-37825400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:37800200-37813400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:37800200-37830200	Weak transcription	Ovary	ovary
21	chr6:37800200-37836200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:37801000-37813600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:37801000-37817600	Weak transcription	Spleen	Spleen
24	chr6:37801000-37818600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:37801200-37833400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:37802400-37818400	Weak transcription	Primary B cells from cord blood	blood
27	chr6:37802600-37818400	Weak transcription	Fetal Lung	lung
28	chr6:37802600-37834400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:37803000-37823800	Weak transcription	Fetal Intestine Large	intestine
30	chr6:37806400-37816000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:37806800-37830800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:37807000-37815800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:37807000-37816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:37808000-37839000	Weak transcription	Fetal Stomach	stomach
35	chr6:37808400-37817600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:37808400-37818000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:37808600-37813400	Weak transcription	Brain Angular Gyrus	brain
38	chr6:37808600-37817800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:37808600-37818200	Weak transcription	Brain Anterior Caudate	brain
40	chr6:37808600-37832600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:37809000-37813400	Weak transcription	GM12878-XiMat	blood
42	chr6:37809400-37823400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:37809600-37813600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:37809600-37825400	Weak transcription	Aorta	Aorta
45	chr6:37810000-37813600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:37810200-37813400	Weak transcription	Psoas Muscle	Psoas
47	chr6:37810200-37817600	Weak transcription	Lung	lung
48	chr6:37810200-37817600	Weak transcription	Right Atrium	heart
49	chr6:37810200-37817600	Weak transcription	Right Ventricle	heart
50	chr6:37810800-37815000	Weak transcription	Left Ventricle	heart

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