Variant report

Variant	rs3737135
Chromosome Location	chr9:86593077-86593078
allele	A/T
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	POLR2A	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
2	HEY1	chr9:86593061-86593424	K562	blood:	n/a	n/a
3	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
5	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
6	NFATC1	chr9:86592763-86594905	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:86592188-86593303	SK-N-SH	brain:	n/a	n/a
8	SIN3A	chr9:86592976-86596804	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFATC1	chr9:86592990-86596378	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:86592943-86593449	Hela-S3	cervix:	n/a	n/a
11	SP1	chr9:86592919-86593574	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr9:86592636-86593161	PFSK-1	brain:	n/a	n/a
13	CHD1	chr9:86592725-86596929	H1-hESC	embryonic stem cell:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
14	POLR2A	chr9:86593040-86596859	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:86593024-86593332	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
2	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
3	chr17:57914983..57917065-chr9:86592190..86594994,2	MCF-7	breast:
4	chr9:86534520..86537940-chr9:86592614..86595774,6	K562	blood:
5	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:

Variant related genes	Relation type
RMI1	TF binding region
HNRNPK	TF binding region
ENSG00000062716	Chromatin interaction
ENSG00000202523	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17086760	0.86[JPT][hapmap]
rs2274915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793477	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55961681	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55978807	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60398007	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62565773	0.81[EUR][1000 genomes]
rs62565777	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62565779	0.80[EUR][1000 genomes]
rs62565780	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62565806	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6559757	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6559758	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7039995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
5	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:86589200-86593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:86590000-86594400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr9:86590600-86593800	Weak transcription	Gastric	stomach
5	chr9:86590600-86594000	Weak transcription	Spleen	Spleen
6	chr9:86590800-86593200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:86590800-86593200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:86590800-86593200	Weak transcription	Esophagus	oesophagus
9	chr9:86590800-86593200	Weak transcription	Lung	lung
10	chr9:86590800-86593200	Weak transcription	Pancreas	Pancrea
11	chr9:86590800-86593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:86590800-86594400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:86591000-86593200	Weak transcription	Small Intestine	intestine
14	chr9:86591000-86593400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:86591000-86594400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
16	chr9:86591200-86593200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:86591200-86593200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:86591200-86594400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
19	chr9:86591400-86593200	Weak transcription	Left Ventricle	heart
20	chr9:86591400-86594400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:86591400-86594600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
22	chr9:86591600-86593600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
23	chr9:86591600-86596600	Active TSS	Ovary	ovary
24	chr9:86591800-86593200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
25	chr9:86591800-86593600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
27	chr9:86592000-86593200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:86592000-86593200	Transcr. at gene 5' and 3'	HepG2	liver
29	chr9:86592000-86594200	Transcr. at gene 5' and 3'	K562	blood
30	chr9:86592200-86593200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:86592200-86593200	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr9:86592200-86593200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:86592200-86593200	Enhancers	Brain Substantia Nigra	brain
34	chr9:86592200-86593600	Transcr. at gene 5' and 3'	NHEK	skin
35	chr9:86592200-86594400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:86592200-86594400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
37	chr9:86592200-86594400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
38	chr9:86592200-86594400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
39	chr9:86592200-86594400	Transcr. at gene 5' and 3'	A549	lung
40	chr9:86592200-86594600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:86592200-86596800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:86592400-86593200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
44	chr9:86592400-86593600	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr9:86592400-86594200	Transcr. at gene 5' and 3'	Osteobl	bone
46	chr9:86592400-86596200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:86592400-86596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr9:86592400-86596600	Active TSS	Aorta	Aorta
49	chr9:86592400-86596800	Active TSS	Right Ventricle	heart
50	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain

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