Variant report

Variant	rs9476810
Chromosome Location	chr6:15251181-15251182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr6:15244739-15251552	IMR90	lung:	n/a	chr6:15245627-15245637 chr6:15245113-15245123
2	POLR2A	chr6:15244299-15251638	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:15211290..15214684-chr6:15251009..15254684,5	K562	blood:
2	chr6:15210948..15212790-chr6:15250679..15252509,2	K562	blood:
3	chr6:15155665..15157322-chr6:15249355..15251263,2	K562	blood:
4	chr6:15249702..15251609-chr6:15440031..15441697,2	MCF-7	breast:
5	chr6:15250579..15252953-chr6:15298506..15301463,2	K562	blood:

Variant related genes	Relation type
JARID2-AS1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10456769	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11751041	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12203689	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2327881	0.83[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap]
rs6915344	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916637	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6934978	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9464779	0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9476806	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15249000-15251800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:15249200-15252400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:15249400-15251200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:15249400-15251800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
5	chr6:15249600-15251200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:15249600-15251400	Weak transcription	Gastric	stomach
7	chr6:15249600-15256200	Weak transcription	Lung	lung
8	chr6:15249800-15251200	Weak transcription	Esophagus	oesophagus
9	chr6:15249800-15251200	Weak transcription	Pancreas	Pancrea
10	chr6:15249800-15251400	Weak transcription	Placenta	Placenta
11	chr6:15249800-15251400	Weak transcription	Left Ventricle	heart
12	chr6:15249800-15251400	Weak transcription	Right Ventricle	heart
13	chr6:15249800-15251600	Weak transcription	Liver	Liver
14	chr6:15249800-15252600	Weak transcription	Spleen	Spleen
15	chr6:15249800-15253400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:15249800-15253600	Weak transcription	Fetal Stomach	stomach
17	chr6:15249800-15256200	Weak transcription	Ovary	ovary
18	chr6:15250000-15251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:15250000-15251800	Enhancers	Fetal Brain Male	brain
20	chr6:15250000-15251800	Enhancers	HepG2	liver
21	chr6:15250000-15252000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:15250000-15252000	Enhancers	Brain Hippocampus Middle	brain
23	chr6:15250000-15252600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:15250000-15252600	Weak transcription	Small Intestine	intestine
25	chr6:15250000-15253000	Weak transcription	Brain Substantia Nigra	brain
26	chr6:15250000-15253600	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:15250000-15253800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:15250000-15254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:15250000-15254000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:15250000-15254000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:15250000-15254000	Weak transcription	Fetal Lung	lung
32	chr6:15250000-15254000	Weak transcription	HSMMtube	muscle
33	chr6:15250000-15254200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:15250000-15254400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:15250000-15255000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:15250000-15255600	Weak transcription	Colonic Mucosa	Colon
37	chr6:15250000-15255600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:15250000-15255600	Weak transcription	Right Atrium	heart
39	chr6:15250000-15256200	Weak transcription	Aorta	Aorta
40	chr6:15250000-15256200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:15250000-15256800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:15250000-15262000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr6:15250200-15251200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:15250200-15251200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr6:15250200-15251200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:15250200-15251200	Weak transcription	Stomach Mucosa	stomach
47	chr6:15250200-15251400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:15250200-15251400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:15250200-15251400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:15250200-15251400	Enhancers	Stomach Smooth Muscle	stomach

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