Variant report

Variant	rs16890181
Chromosome Location	chr6:37794108-37794109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37793853..37796744-chr6:37803996..37806760,2	K562	blood:
2	chr6:37784606..37792959-chr6:37792982..37799004,11	MCF-7	breast:
3	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: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10485030	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs10498739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10498740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10947702	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10947704	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11750950	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11751781	0.86[CHB][hapmap]
rs11751962	0.82[ASN][1000 genomes]
rs11752521	0.86[CHB][hapmap]
rs11752863	0.84[ASN][1000 genomes]
rs11753054	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11755095	0.82[ASN][1000 genomes]
rs11755629	0.86[CHB][hapmap]
rs11756713	0.86[CHB][hapmap]
rs11757161	0.82[ASN][1000 genomes]
rs11759496	0.81[ASN][1000 genomes]
rs11759826	0.86[CHB][hapmap]
rs11967129	0.82[ASN][1000 genomes]
rs12660498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12660773	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes]
rs12660922	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12661109	1.00[AMR][1000 genomes]
rs12661378	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12661480	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12661702	0.82[ASN][1000 genomes]
rs12662305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12662426	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12662823	1.00[AMR][1000 genomes]
rs12663957	1.00[AMR][1000 genomes]
rs12664091	0.85[CHB][hapmap]
rs12664768	0.86[CHB][hapmap]
rs13195545	0.82[ASN][1000 genomes]
rs13205311	0.82[ASN][1000 genomes]
rs13206035	0.85[CHB][hapmap]
rs16890168	0.87[JPT][hapmap]
rs16890175	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs16890177	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16890215	1.00[CHB][hapmap];1.00[JPT][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];0.86[ASN][1000 genomes]
rs16890298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890301	0.90[CHB][hapmap]
rs16890305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs16890307	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs16890309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2025431	0.82[ASN][1000 genomes]
rs2064795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2273441	0.85[CHB][hapmap]
rs2274090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2274091	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2395689	0.90[CHB][hapmap]
rs2842510	0.85[CHB][hapmap]
rs2842511	0.90[CHB][hapmap]
rs2842521	0.85[CHB][hapmap]
rs35122358	0.82[ASN][1000 genomes]
rs35216205	0.82[ASN][1000 genomes]
rs3844314	0.86[CHB][hapmap]
rs3852216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56093219	0.83[ASN][1000 genomes]
rs57198506	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57276677	0.87[ASN][1000 genomes]
rs57402213	0.81[ASN][1000 genomes]
rs57458792	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57911756	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58084785	1.00[AMR][1000 genomes]
rs58320470	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58473303	1.00[AMR][1000 genomes]
rs58692659	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59036086	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59103990	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59649654	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59859268	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60141491	1.00[ASN][1000 genomes]
rs60284537	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60404082	1.00[AMR][1000 genomes]
rs60508820	1.00[AMR][1000 genomes]
rs60637081	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60883115	1.00[AMR][1000 genomes]
rs61090283	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61108907	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61277916	1.00[AMR][1000 genomes]
rs61332486	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61466900	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6458032	0.86[CHB][hapmap]
rs6906289	0.80[CHB][hapmap]
rs6911716	0.86[CHB][hapmap]
rs72849341	0.83[ASN][1000 genomes]
rs73421436	0.84[ASN][1000 genomes]
rs73421439	0.84[ASN][1000 genomes]
rs752110	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7739801	0.94[CHB][hapmap]
rs7742226	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7746266	0.85[CHB][hapmap]
rs7748312	0.86[CHB][hapmap]
rs7756261	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs7759145	0.82[ASN][1000 genomes]
rs7759792	0.85[CHB][hapmap]
rs7761561	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs7764130	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7773419	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7775794	0.86[CHB][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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37789000-37794400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:37789000-37796400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:37789400-37800000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:37790800-37794800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:37790800-37799200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:37791000-37795400	Weak transcription	Hela-S3	cervix
7	chr6:37791000-37798000	Weak transcription	HSMM	muscle
8	chr6:37791000-37799200	Weak transcription	Esophagus	oesophagus
9	chr6:37791000-37800400	Weak transcription	Thymus	Thymus
10	chr6:37791200-37795000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:37791200-37795400	Weak transcription	Fetal Kidney	kidney
12	chr6:37791200-37795400	Weak transcription	HSMMtube	muscle
13	chr6:37791200-37798000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:37791200-37800000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:37791400-37794200	Weak transcription	Colonic Mucosa	Colon
17	chr6:37791400-37794800	Weak transcription	Primary B cells from cord blood	blood
18	chr6:37791400-37794800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:37791400-37794800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:37791400-37794800	Weak transcription	NHLF	lung
21	chr6:37791400-37795200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:37791400-37795400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:37791400-37795400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:37791400-37795400	Weak transcription	Brain Anterior Caudate	brain
25	chr6:37791400-37795400	Weak transcription	Spleen	Spleen
26	chr6:37791400-37795600	Weak transcription	Fetal Stomach	stomach
27	chr6:37791400-37796000	Enhancers	Liver	Liver
28	chr6:37791400-37796400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:37791400-37799200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:37791400-37799200	Weak transcription	Pancreas	Pancrea
31	chr6:37791400-37799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:37791400-37799400	Weak transcription	Aorta	Aorta
33	chr6:37791400-37800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:37791400-37800400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:37791400-37801800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:37791400-37801800	Weak transcription	Fetal Brain Female	brain
37	chr6:37791400-37801800	Weak transcription	A549	lung
38	chr6:37791400-37810200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:37791600-37794200	Enhancers	Fetal Intestine Large	intestine
42	chr6:37791600-37794800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:37791600-37795000	Weak transcription	Fetal Lung	lung
44	chr6:37791600-37795200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:37791600-37795400	Weak transcription	NHEK	skin
46	chr6:37791600-37795600	Weak transcription	Brain Angular Gyrus	brain
47	chr6:37791600-37795800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:37791600-37797400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:37791600-37797400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:37791600-37797400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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