Variant report

Variant	rs2001994
Chromosome Location	chr9:96393849-96393850
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96393648..96395801-chr9:96402500..96404793,2	MCF-7	breast:
2	chr9:96389762..96391845-chr9:96392211..96394395,2	K562	blood:
3	chr9:96391831..96394155-chr9:96413684..96415869,2	K562	blood:
4	chr9:96385198..96387004-chr9:96393310..96394874,2	MCF-7	breast:
5	chr9:96338187..96341203-chr9:96391174..96393981,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10761247	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10761251	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761252	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761254	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761255	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821196	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992807	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10992836	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992841	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992854	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1806458	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398851	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398853	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398855	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2398861	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3750358	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750362	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763605	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743930	0.87[ASN][1000 genomes]
rs4743931	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs4744264	0.82[ASN][1000 genomes]
rs6479499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479500	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479501	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7019745	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7024028	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7028306	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7849752	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv519449	chr9:96382100-96395429	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96374600-96399800	Weak transcription	K562	blood
2	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:96380800-96399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96384000-96396400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
6	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:96387200-96399800	Weak transcription	Fetal Heart	heart
8	chr9:96387600-96399600	Weak transcription	Fetal Kidney	kidney
9	chr9:96390200-96398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:96390200-96405400	Weak transcription	HepG2	liver
11	chr9:96390400-96395200	Weak transcription	NHLF	lung
12	chr9:96390400-96398600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:96390400-96399400	Weak transcription	Hela-S3	cervix
14	chr9:96390600-96395200	Weak transcription	Brain Substantia Nigra	brain
15	chr9:96390600-96397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:96390600-96398200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:96390600-96398400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:96390600-96399000	Weak transcription	Osteobl	bone
19	chr9:96390600-96399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:96390800-96396800	Weak transcription	NHEK	skin
21	chr9:96390800-96398400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:96390800-96398600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:96391400-96398800	Strong transcription	Fetal Intestine Small	intestine
24	chr9:96391400-96400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:96391600-96395800	Strong transcription	Fetal Thymus	thymus
26	chr9:96391600-96398400	Strong transcription	Thymus	Thymus
27	chr9:96391600-96398600	Strong transcription	Fetal Intestine Large	intestine
28	chr9:96391600-96398800	Strong transcription	Aorta	Aorta
29	chr9:96391600-96399600	Strong transcription	Primary T cells from cord blood	blood
30	chr9:96391600-96399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:96391600-96400200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:96391600-96400200	Strong transcription	Gastric	stomach
33	chr9:96391600-96402000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:96391800-96398800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:96391800-96399000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:96391800-96399000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:96391800-96400000	Strong transcription	Colonic Mucosa	Colon
38	chr9:96391800-96400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:96391800-96400400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:96391800-96402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:96391800-96402400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:96391800-96402400	Strong transcription	Placenta	Placenta
43	chr9:96392000-96394000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr9:96392000-96396800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:96392000-96396800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:96392000-96397000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr9:96392000-96397200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:96392000-96397200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:96392000-96397400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:96392000-96398000	Strong transcription	Primary monocytes fromperipheralblood	blood

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