Variant report

Variant	rs1412988
Chromosome Location	chr9:71397734-71397735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71397068..71400120-chr9:71405362..71406999,3	MCF-7	breast:
2	chr9:71397331..71400852-chr9:71402232..71407061,5	K562	blood:
3	chr9:71347274..71349362-chr9:71397346..71399719,2	K562	blood:
4	chr9:71395139..71397780-chr9:71401800..71403329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236998	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10115536	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10117946	0.82[ASN][1000 genomes]
rs10781232	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs10869404	0.86[ASN][1000 genomes]
rs11143802	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12686613	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1414946	0.81[ASN][1000 genomes]
rs17057642	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17057918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17081050	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1889937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2027024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2039425	0.89[ASN][1000 genomes]
rs2039625	0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2151421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2151422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3750377	0.99[ASN][1000 genomes]
rs4237268	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4259475	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4745321	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4745351	0.82[ASN][1000 genomes]
rs4745359	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6560398	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7019684	0.90[ASN][1000 genomes]
rs7032651	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7035999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7039817	0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7041004	0.95[GIH][hapmap]
rs7046284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs72512921	0.98[ASN][1000 genomes]
rs7851399	0.88[ASN][1000 genomes]
rs7861710	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7865412	0.92[ASN][1000 genomes]
rs7869452	0.92[ASN][1000 genomes]
rs975123	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71395200-71397800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:71395600-71400200	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr9:71395800-71398800	Enhancers	Small Intestine	intestine
4	chr9:71395800-71400200	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:71396000-71397800	Enhancers	Brain Substantia Nigra	brain
6	chr9:71396000-71398000	Enhancers	Stomach Mucosa	stomach
7	chr9:71396000-71398600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:71396000-71399000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:71396000-71399000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:71396000-71399200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:71396000-71400400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr9:71396000-71402400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:71396000-71403400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:71396200-71397800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:71396200-71397800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:71396200-71397800	Enhancers	Hela-S3	cervix
18	chr9:71396200-71398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:71396200-71398000	Enhancers	Fetal Stomach	stomach
20	chr9:71396200-71398000	Enhancers	Osteobl	bone
21	chr9:71396200-71398800	Enhancers	Fetal Intestine Large	intestine
22	chr9:71396200-71399000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:71396200-71399000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr9:71396200-71399000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:71396200-71399000	Enhancers	HUVEC	blood vessel
26	chr9:71396200-71399200	Enhancers	Primary hematopoietic stem cells	blood
27	chr9:71396200-71399200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr9:71396200-71399600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:71396200-71400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:71396200-71400800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr9:71396200-71400800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr9:71396200-71400800	Enhancers	Brain Hippocampus Middle	brain
33	chr9:71396200-71400800	Enhancers	Fetal Heart	heart
34	chr9:71396200-71401000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr9:71396200-71401000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:71396400-71397800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr9:71396400-71398200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:71396400-71398800	Enhancers	NHDF-Ad	bronchial
40	chr9:71396400-71399000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:71396400-71399000	Enhancers	HepG2	liver
42	chr9:71396400-71400200	Enhancers	Colon Smooth Muscle	Colon
43	chr9:71396600-71397800	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr9:71396600-71398200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:71396600-71398200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr9:71396600-71398600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:71396600-71398600	Enhancers	Fetal Intestine Small	intestine
48	chr9:71396600-71399000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:71396600-71399000	Enhancers	Fetal Thymus	thymus
50	chr9:71396600-71399200	Flanking Active TSS	Fetal Brain Female	brain

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