Variant report

Variant	rs12236743
Chromosome Location	chr9:86250412-86250413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86249957..86252559-chr9:86321303..86324119,2	MCF-7	breast:
2	chr9:86247178..86252278-chr9:86254565..86260519,7	MCF-7	breast:
3	chr9:86249075..86251124-chr9:86419195..86422058,2	K562	blood:
4	chr9:86248664..86251363-chr9:86251483..86253533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11140175	0.90[ASN][1000 genomes]
rs11140178	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140179	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140182	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140191	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140197	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11140215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140217	1.00[EUR][1000 genomes]
rs11140219	1.00[EUR][1000 genomes]
rs11140225	1.00[EUR][1000 genomes]
rs11140228	1.00[EUR][1000 genomes]
rs11140229	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140230	0.92[EUR][1000 genomes]
rs11140235	1.00[EUR][1000 genomes]
rs11140238	1.00[CEU][hapmap]
rs11140248	1.00[EUR][1000 genomes]
rs11140250	1.00[EUR][1000 genomes]
rs11140252	1.00[EUR][1000 genomes]
rs11140254	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140257	1.00[EUR][1000 genomes]
rs11140258	1.00[EUR][1000 genomes]
rs11140266	0.92[EUR][1000 genomes]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11559387	0.85[EUR][1000 genomes]
rs11560627	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12235151	0.92[EUR][1000 genomes]
rs12235969	1.00[CEU][hapmap]
rs12236455	0.92[EUR][1000 genomes]
rs12237262	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12237555	1.00[EUR][1000 genomes]
rs12238365	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12238575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780985	1.00[CHB][hapmap]
rs28627139	1.00[EUR][1000 genomes]
rs28655802	0.86[EUR][1000 genomes]
rs3763626	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv973848	chr9:86241130-86260149	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86238600-86265000	Weak transcription	Ovary	ovary
2	chr9:86238800-86254600	Weak transcription	Left Ventricle	heart
3	chr9:86238800-86260600	Weak transcription	Right Ventricle	heart
4	chr9:86238800-86264600	Weak transcription	Psoas Muscle	Psoas
5	chr9:86239000-86264800	Weak transcription	HMEC	breast
6	chr9:86239000-86265200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:86239200-86261000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:86239400-86254400	Weak transcription	Brain Anterior Caudate	brain
9	chr9:86239400-86254400	Weak transcription	Brain Substantia Nigra	brain
10	chr9:86239400-86266200	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:86239400-86266400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:86239600-86260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:86239600-86260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:86239600-86265000	Weak transcription	HUVEC	blood vessel
15	chr9:86239600-86266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:86239800-86266800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:86240200-86265000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:86240400-86254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:86242200-86256600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:86242400-86253800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:86242400-86257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:86242400-86264800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:86242600-86265000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr9:86243200-86260800	Weak transcription	Primary B cells from cord blood	blood
26	chr9:86243200-86261000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:86243200-86269600	Weak transcription	Pancreas	Pancrea
28	chr9:86243600-86264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr9:86243600-86266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:86244000-86260600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:86244000-86260800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:86244200-86264600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:86244400-86254200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:86244400-86262200	Weak transcription	A549	lung
35	chr9:86244400-86264600	Weak transcription	NHLF	lung
36	chr9:86244600-86257600	Weak transcription	Lung	lung
37	chr9:86244600-86257800	Weak transcription	Primary T cells from cord blood	blood
38	chr9:86244600-86258000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:86244600-86260000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:86244600-86260200	Weak transcription	NHEK	skin
41	chr9:86244800-86254400	Weak transcription	HSMM	muscle
42	chr9:86244800-86258200	Weak transcription	GM12878-XiMat	blood
43	chr9:86244800-86260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:86244800-86260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:86244800-86261200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:86244800-86278800	Weak transcription	Spleen	Spleen
47	chr9:86244800-86285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:86245000-86250600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:86245000-86252200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:86245000-86257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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