Variant report

Variant	rs10988717
Chromosome Location	chr9:101888785-101888786
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:101888680-101888880	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:101888681-101888969	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:101888254-101888983	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101866361..101869341-chr9:101886452..101890095,3	MCF-7	breast:
2	chr9:101865542..101868917-chr9:101887238..101894962,8	MCF-7	breast:
3	chr9:101887374..101889321-chr9:101890165..101891721,2	MCF-7	breast:
4	chr9:101766336..101770748-chr9:101884242..101889062,4	K562	blood:
5	chr9:101835981..101841797-chr9:101884108..101889285,8	K562	blood:
6	chr9:101882379..101885644-chr9:101887362..101889635,3	MCF-7	breast:

No data

Variant related genes	Relation type
TGFBR1	TF binding region
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10733708	0.82[ASN][1000 genomes]
rs10733709	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs10739778	0.81[ASN][1000 genomes]
rs10760668	0.92[ASN][1000 genomes]
rs10760669	0.94[ASN][1000 genomes]
rs10760670	0.82[ASN][1000 genomes]
rs10760671	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10760672	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10760673	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10760674	0.89[ASN][1000 genomes]
rs10819636	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10819638	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10819640	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10988706	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10988709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988713	0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10988715	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988716	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10988723	0.89[ASN][1000 genomes]
rs11568752	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11568753	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11568770	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11568778	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12346650	0.95[CHB][hapmap]
rs12685571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12686782	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1571589	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs1590	0.80[ASN][1000 genomes]
rs1699413	0.91[ASN][1000 genomes]
rs1888225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973518	0.89[ASN][1000 genomes]
rs2026811	0.81[ASN][1000 genomes]
rs334348	0.80[ASN][1000 genomes]
rs334349	0.80[ASN][1000 genomes]
rs334351	0.94[ASN][1000 genomes]
rs334353	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs334354	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs334355	0.81[ASN][1000 genomes]
rs334362	0.92[ASN][1000 genomes]
rs334363	0.90[ASN][1000 genomes]
rs334364	0.90[ASN][1000 genomes]
rs334366	0.90[ASN][1000 genomes]
rs334367	0.90[ASN][1000 genomes]
rs334370	0.88[ASN][1000 genomes]
rs3739798	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs44466	0.86[ASN][1000 genomes]
rs597457	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6478972	0.82[ASN][1000 genomes]
rs6478973	0.94[ASN][1000 genomes]
rs7031302	0.82[ASN][1000 genomes]
rs7031309	0.82[ASN][1000 genomes]
rs7041311	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs7042852	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs7043624	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs7874221	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101868400-101896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:101868600-101889800	Weak transcription	Ovary	ovary
3	chr9:101868600-101894400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:101870000-101908600	Weak transcription	Brain Germinal Matrix	brain
5	chr9:101870600-101889800	Weak transcription	NHLF	lung
6	chr9:101874600-101889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:101875600-101894600	Weak transcription	Spleen	Spleen
8	chr9:101876400-101889400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:101876600-101904200	Weak transcription	Liver	Liver
10	chr9:101877000-101889400	Weak transcription	HSMMtube	muscle
11	chr9:101878000-101897400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:101878800-101891800	Weak transcription	Fetal Stomach	stomach
13	chr9:101878800-101892400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:101878800-101903200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:101882000-101892600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr9:101882000-101893400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:101882000-101893400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr9:101882000-101895000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr9:101882200-101889200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:101882200-101889400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:101882200-101901400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr9:101882200-101903000	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:101882400-101893200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:101882400-101894600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:101882800-101889200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:101883000-101889800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:101883000-101900000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:101884000-101889000	Weak transcription	Primary B cells from cord blood	blood
29	chr9:101884400-101891200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:101884400-101892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:101884600-101897200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr9:101884800-101889200	Weak transcription	Small Intestine	intestine
33	chr9:101884800-101894400	Weak transcription	Aorta	Aorta
34	chr9:101885000-101889200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:101885000-101889800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:101885000-101891000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr9:101885200-101889200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:101885200-101890400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr9:101885200-101891400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:101885200-101896800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:101885200-101901600	Weak transcription	A549	lung
42	chr9:101885600-101889400	Enhancers	K562	blood
43	chr9:101885600-101889600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:101885600-101891200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:101885800-101890200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr9:101886000-101888800	Enhancers	Fetal Brain Male	brain
47	chr9:101886200-101891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:101886400-101892400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:101886600-101889200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:101886600-101890000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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