Variant report

Variant	rs1889937
Chromosome Location	chr9:71403106-71403107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71400597..71404451-chr9:71406708..71409668,4	MCF-7	breast:
2	chr9:71395139..71397780-chr9:71401800..71403329,2	MCF-7	breast:
3	chr9:71401239..71403328-chr9:71403881..71406590,2	K562	blood:

Variant related genes	Relation type
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 44 )
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	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs10869404	0.86[ASN][1000 genomes]
rs11143802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12000088	0.80[EUR][1000 genomes]
rs12686613	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1412988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1556751	0.81[CEU][hapmap]
rs17057642	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17057918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17081050	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2017	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2027024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2039425	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2039625	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs2151421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2151422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3750377	0.97[ASN][1000 genomes]
rs4237268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4259475	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4745321	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4745359	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6560398	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7019684	0.90[ASN][1000 genomes]
rs7032651	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs7035999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7039817	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7046284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs72512921	0.95[ASN][1000 genomes]
rs7851399	0.88[ASN][1000 genomes]
rs7861710	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7865412	0.92[ASN][1000 genomes]
rs7869452	0.92[ASN][1000 genomes]
rs975123	1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71396000-71403400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:71397200-71403800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:71397200-71404200	Weak transcription	Esophagus	oesophagus
6	chr9:71397200-71409600	Weak transcription	Colonic Mucosa	Colon
7	chr9:71397200-71417400	Weak transcription	Lung	lung
8	chr9:71397800-71408000	Weak transcription	Gastric	stomach
9	chr9:71398600-71404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:71398600-71405400	Strong transcription	Primary B cells from cord blood	blood
11	chr9:71398800-71406000	Weak transcription	Spleen	Spleen
12	chr9:71398800-71408000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:71398800-71409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:71399000-71403800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:71399000-71404000	Weak transcription	Ovary	ovary
16	chr9:71399000-71405600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:71399000-71406200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:71399000-71408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:71399000-71408400	Weak transcription	Stomach Mucosa	stomach
20	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
21	chr9:71399200-71407800	Weak transcription	GM12878-XiMat	blood
22	chr9:71399400-71404800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:71399600-71407200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:71399800-71413200	Weak transcription	Dnd41	blood
25	chr9:71400200-71403200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:71400200-71405800	Weak transcription	Brain Angular Gyrus	brain
27	chr9:71400200-71406000	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:71400400-71403600	Weak transcription	Right Ventricle	heart
29	chr9:71400400-71404600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:71400400-71408000	Weak transcription	K562	blood
31	chr9:71400400-71408600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:71400600-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:71400800-71403600	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:71400800-71403800	Weak transcription	Right Atrium	heart
35	chr9:71400800-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:71400800-71409000	Weak transcription	Adipose Nuclei	Adipose
37	chr9:71400800-71409000	Weak transcription	Small Intestine	intestine
38	chr9:71401000-71403200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr9:71401000-71404600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr9:71401000-71404800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:71401000-71407000	Weak transcription	Brain Germinal Matrix	brain
42	chr9:71401600-71405000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr9:71401800-71404400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr9:71401800-71404600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:71401800-71404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:71401800-71405000	Strong transcription	Fetal Intestine Small	intestine
47	chr9:71402000-71403200	Enhancers	Pancreas	Pancrea
48	chr9:71402000-71405400	Weak transcription	Aorta	Aorta
49	chr9:71402200-71403600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:71402400-71403800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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