Variant report

Variant	rs10820938
Chromosome Location	chr9:94841980-94841981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94840392..94843786-chr9:94877379..94879314,3	MCF-7	breast:
2	chr9:94839775..94842197-chr9:94842980..94845500,2	K562	blood:
3	chr9:94500963..94503336-chr9:94841950..94843552,2	K562	blood:

Variant related genes	Relation type
ENSG00000090054	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10115684	0.86[CEU][hapmap]
rs10116326	0.87[CEU][hapmap]
rs10820926	0.85[CEU][hapmap]
rs10820935	0.84[ASN][1000 genomes]
rs10992177	0.85[CEU][hapmap]
rs10992178	0.85[CEU][hapmap]
rs10992212	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs10992215	0.84[ASN][1000 genomes]
rs10992216	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs10992220	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10992221	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10992222	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992230	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10992233	0.86[ASN][1000 genomes]
rs10992234	0.82[MEX][hapmap]
rs11533009	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12235309	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12235310	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12235495	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12237221	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12237598	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs12238682	0.82[ASN][1000 genomes]
rs12337180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343974	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16907979	0.85[CEU][hapmap]
rs16908021	0.85[CEU][hapmap]
rs16908135	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16908137	0.82[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1970121	0.82[MEX][hapmap]
rs2001917	0.87[CEU][hapmap]
rs2096388	0.80[ASN][1000 genomes]
rs3858090	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4518728	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58909848	0.84[ASN][1000 genomes]
rs59114373	0.81[AMR][1000 genomes]
rs59183854	0.84[ASN][1000 genomes]
rs59856128	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7022553	0.83[ASN][1000 genomes]
rs7029539	0.82[MEX][hapmap]
rs7033030	0.80[ASN][1000 genomes]
rs7042585	0.85[CEU][hapmap]
rs7847966	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7849220	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7852067	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7856177	0.82[MEX][hapmap]
rs7858659	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs7862826	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7872515	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
3	chr9:94820600-94844400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
5	chr9:94823200-94842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:94823200-94844400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:94824000-94843600	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr9:94824000-94844000	Strong transcription	Primary B cells from cord blood	blood
9	chr9:94824000-94860400	Weak transcription	Psoas Muscle	Psoas
10	chr9:94824800-94844200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:94825400-94844200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:94825600-94844200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:94825600-94844400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr9:94826400-94843000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:94826600-94843800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr9:94826800-94844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:94826800-94844400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:94826800-94844400	Strong transcription	Primary T cells from cord blood	blood
19	chr9:94827000-94843400	Strong transcription	Thymus	Thymus
20	chr9:94827000-94844000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:94827200-94856800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:94827400-94844000	Strong transcription	Liver	Liver
23	chr9:94827800-94843200	Strong transcription	Fetal Stomach	stomach
24	chr9:94827800-94843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:94828400-94842600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:94828400-94842800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:94828600-94844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:94828800-94850600	Weak transcription	Fetal Brain Male	brain
29	chr9:94828800-94850600	Weak transcription	Fetal Kidney	kidney
30	chr9:94829000-94862600	Weak transcription	Hela-S3	cervix
31	chr9:94830000-94845200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:94830000-94850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:94830000-94856800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:94830200-94856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:94830200-94857000	Weak transcription	HUVEC	blood vessel
36	chr9:94830200-94860400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:94830800-94850200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr9:94831000-94842400	Strong transcription	Fetal Muscle Leg	muscle
40	chr9:94831000-94843000	Strong transcription	Fetal Intestine Small	intestine
41	chr9:94831200-94844000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:94831600-94843400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:94832400-94850600	Weak transcription	A549	lung
44	chr9:94832600-94843000	Weak transcription	NHDF-Ad	bronchial
45	chr9:94832800-94842000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:94832800-94842000	Weak transcription	Small Intestine	intestine
47	chr9:94833000-94845800	Weak transcription	Brain Substantia Nigra	brain
48	chr9:94833000-94857000	Weak transcription	Brain Anterior Caudate	brain
49	chr9:94833000-94858000	Weak transcription	Brain Angular Gyrus	brain
50	chr9:94833400-94843000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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