Variant report

Variant	rs10840263
Chromosome Location	chr11:9601433-9601434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:9600579-9604393	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:9601406-9604955	K562	blood:	n/a	n/a
3	POLR2A	chr11:9600748-9604031	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:9600600-9602895	K562	blood:	n/a	n/a
5	POLR2A	chr11:9600706-9604075	PBDE	blood:	n/a	n/a
6	POLR2A	chr11:9600697-9604836	K562	blood:	n/a	n/a
7	POLR2A	chr11:9600726-9601924	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:9599736-9604122	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:9600678-9604729	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:9600605-9604108	IMR90	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:9600849..9601578-chr14:24886578..24887287,2	MCF-7	breast:
2	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
3	chr11:9597254..9599357-chr11:9599968..9601981,3	MCF-7	breast:
4	chr11:9601269..9603946-chr11:9604466..9607309,2	MCF-7	breast:
5	chr11:9483118..9484824-chr11:9600066..9602856,2	K562	blood:

No data

Variant related genes	Relation type
WEE1	TF binding region
RN7SL56P	TF binding region
ENSG00000166478	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000243964	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1049403	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10770041	0.97[ASN][1000 genomes]
rs10770042	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840265	0.88[ASN][1000 genomes]
rs10840266	0.89[ASN][1000 genomes]
rs11042426	0.80[EUR][1000 genomes]
rs11042429	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[ASN][1000 genomes]
rs11042431	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12799030	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35981065	0.87[EUR][1000 genomes]
rs4910482	0.97[ASN][1000 genomes]
rs7107252	0.89[ASN][1000 genomes]
rs7110225	0.92[ASN][1000 genomes]
rs7131557	0.90[EUR][1000 genomes]
rs7940672	0.86[EUR][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	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840263	SWAP70	cis	lymphoblastoid	seeQTL
rs10840263	DKK3	cis	cerebellum	SCAN
rs10840263	OR2D3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9596800-9604000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:9597000-9604600	Weak transcription	Lung	lung
3	chr11:9597000-9606000	Weak transcription	Small Intestine	intestine
4	chr11:9597000-9613400	Weak transcription	Gastric	stomach
5	chr11:9597000-9622000	Weak transcription	Spleen	Spleen
6	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
7	chr11:9597600-9601800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:9597600-9602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:9597600-9602400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:9597600-9604200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:9597600-9609600	Weak transcription	Brain Anterior Caudate	brain
12	chr11:9597600-9615200	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:9597800-9603400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:9597800-9604600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:9597800-9605600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr11:9598000-9605600	Weak transcription	Stomach Mucosa	stomach
17	chr11:9598400-9612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:9598600-9608800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:9598600-9610800	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr11:9598800-9611600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr11:9599200-9606200	Weak transcription	Fetal Brain Male	brain
22	chr11:9599200-9608400	Weak transcription	Adipose Nuclei	Adipose
23	chr11:9599200-9612200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:9599400-9601600	Weak transcription	Left Ventricle	heart
25	chr11:9599400-9602400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:9599400-9602600	Weak transcription	Primary B cells from cord blood	blood
27	chr11:9599400-9603400	Weak transcription	Fetal Brain Female	brain
28	chr11:9599400-9603400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:9599400-9605800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:9599400-9606000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:9599400-9608600	Weak transcription	Psoas Muscle	Psoas
32	chr11:9599400-9610000	Weak transcription	Esophagus	oesophagus
33	chr11:9599400-9612200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr11:9599400-9612400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr11:9599400-9612400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:9599400-9612400	Strong transcription	Fetal Thymus	thymus
37	chr11:9599600-9602400	Weak transcription	Brain Germinal Matrix	brain
38	chr11:9599600-9602400	Weak transcription	Thymus	Thymus
39	chr11:9599600-9603000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:9599600-9603400	Weak transcription	Ovary	ovary
41	chr11:9599600-9605800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:9599600-9606000	Weak transcription	Right Ventricle	heart
43	chr11:9599600-9607800	Weak transcription	Primary T cells from cord blood	blood
44	chr11:9599600-9608000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr11:9599600-9609800	Weak transcription	Colonic Mucosa	Colon
46	chr11:9599600-9610000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:9599600-9610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr11:9599600-9611200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:9599600-9622800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:9599800-9601600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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