Variant report

Variant	rs12238575
Chromosome Location	chr9:86309948-86309949
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86309310..86311288-chr9:86311516..86313042,2	K562	blood:
2	chr9:86304049..86306359-chr9:86307807..86310071,2	K562	blood:
3	chr9:86308775..86310680-chr9:86314614..86316795,2	MCF-7	breast:
4	chr9:86303158..86305549-chr9:86307402..86310035,3	K562	blood:

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

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

rs_ID	r²[population]
rs11140178	0.85[EUR][1000 genomes]
rs11140179	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140182	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140191	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140197	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140217	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140219	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140225	1.00[EUR][1000 genomes];0.93[ASN][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]
rs11140280	1.00[CEU][hapmap]
rs11559387	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11560627	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12235151	0.92[EUR][1000 genomes]
rs12235969	1.00[CEU][hapmap]
rs12236455	0.92[EUR][1000 genomes]
rs12236743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12237262	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12237555	1.00[EUR][1000 genomes]
rs12238365	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[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];0.93[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	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
2	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
3	chr9:86293600-86317000	Weak transcription	NHLF	lung
4	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:86294200-86314200	Weak transcription	Gastric	stomach
6	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
7	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:86295000-86313600	Weak transcription	Lung	lung
9	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
10	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:86296800-86314200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:86297000-86315600	Weak transcription	HMEC	breast
13	chr9:86297000-86315600	Weak transcription	HSMM	muscle
14	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:86297600-86310800	Weak transcription	Fetal Lung	lung
16	chr9:86297600-86314400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:86297600-86319800	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:86297800-86311600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:86297800-86314800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:86297800-86315800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:86298000-86313600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:86298000-86314200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:86298000-86315400	Weak transcription	HepG2	liver
25	chr9:86298000-86315600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:86298000-86316600	Weak transcription	Thymus	Thymus
27	chr9:86298000-86316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
29	chr9:86298200-86311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:86298200-86317000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:86298200-86317600	Weak transcription	Dnd41	blood
32	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
34	chr9:86299600-86313600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:86299600-86319400	Weak transcription	Fetal Stomach	stomach
36	chr9:86299600-86320000	Weak transcription	Fetal Intestine Small	intestine
37	chr9:86300000-86310800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:86300000-86313800	Weak transcription	HUVEC	blood vessel
39	chr9:86300200-86313000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:86300200-86313000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:86300200-86313000	Weak transcription	A549	lung
42	chr9:86300200-86314400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:86300400-86312000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:86300400-86315600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:86300400-86320400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:86300600-86310600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr9:86300600-86312800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:86300600-86320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:86300800-86316600	Weak transcription	NHEK	skin
50	chr9:86301000-86310000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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