Variant report

Variant	rs794778
Chromosome Location	chr6:15290663-15290664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15288261..15289953-chr6:15290312..15293212,2	K562	blood:
2	chr6:15268694..15271371-chr6:15290123..15292738,2	K562	blood:
3	chr6:15253215..15254764-chr6:15288126..15290824,2	K562	blood:
4	chr6:15287052..15289953-chr6:15290312..15293224,4	K562	blood:
5	chr6:15245710..15248357-chr6:15290228..15292278,2	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2282823	1.00[JPT][hapmap]
rs2299055	1.00[JPT][hapmap]
rs3857641	0.82[YRI][hapmap]
rs3915734	0.81[JPT][hapmap]
rs56156626	0.90[AFR][1000 genomes]
rs58053975	0.90[AFR][1000 genomes]
rs707828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs707836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs707838	0.81[CHB][hapmap]
rs707839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73361549	0.92[AFR][1000 genomes]
rs73361569	0.90[AFR][1000 genomes]
rs794775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794776	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs794777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794784	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794786	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs794788	0.81[CHB][hapmap]
rs794789	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs794792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794793	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs794795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794797	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9383048	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv601006	chr6:15275305-15300590	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15276800-15293200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:15277200-15294000	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:15280200-15293800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:15281400-15293400	Weak transcription	Esophagus	oesophagus
5	chr6:15281400-15296400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:15281600-15294000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:15281800-15293400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:15281800-15300200	Weak transcription	Fetal Stomach	stomach
9	chr6:15282400-15299400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:15282600-15296400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:15285200-15296000	Weak transcription	Liver	Liver
12	chr6:15285200-15296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:15285200-15299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:15285200-15299400	Weak transcription	A549	lung
15	chr6:15285400-15291600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:15285800-15299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:15285800-15299800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:15286200-15296200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:15286400-15291600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:15286400-15291800	Weak transcription	HSMM	muscle
21	chr6:15286400-15293600	Weak transcription	HSMMtube	muscle
22	chr6:15286400-15299400	Weak transcription	NHEK	skin
23	chr6:15286400-15299600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:15286800-15299200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:15287600-15291000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr6:15287800-15290800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:15287800-15292000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:15288400-15291000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:15288400-15292800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:15288400-15293200	Weak transcription	Primary T cells from cord blood	blood
31	chr6:15288400-15293400	Weak transcription	Pancreas	Pancrea
32	chr6:15288400-15293800	Weak transcription	Brain Germinal Matrix	brain
33	chr6:15288600-15290800	Enhancers	HepG2	liver
34	chr6:15288600-15291000	Enhancers	Brain Hippocampus Middle	brain
35	chr6:15288600-15293200	Weak transcription	Thymus	Thymus
36	chr6:15288800-15290800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:15288800-15290800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr6:15288800-15299000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:15288800-15299600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:15289000-15299200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:15289200-15290800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr6:15289200-15290800	Enhancers	Adipose Nuclei	Adipose
43	chr6:15289200-15292600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:15289200-15293200	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:15289400-15290800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:15289400-15291200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:15289400-15291600	Weak transcription	Brain Anterior Caudate	brain
48	chr6:15289400-15291800	Weak transcription	Spleen	Spleen
49	chr6:15289400-15292800	Weak transcription	Left Ventricle	heart
50	chr6:15289400-15293000	Weak transcription	H1 Cell Line	embryonic stem cell

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