Variant report

Variant	rs3109959
Chromosome Location	chr4:107231078-107231079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:107226289..107231817-chr4:107234990..107238909,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164022	Chromatin interaction
ENSG00000145348	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10004034	0.96[ASN][1000 genomes]
rs10017707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10025668	0.82[ASN][1000 genomes]
rs10516530	0.95[ASN][1000 genomes]
rs10516531	0.95[ASN][1000 genomes]
rs11097923	0.96[ASN][1000 genomes]
rs1134648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11938792	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508029	0.93[ASN][1000 genomes]
rs12512475	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17036581	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2691805	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691806	0.98[ASN][1000 genomes]
rs2728176	0.98[ASN][1000 genomes]
rs2728177	0.98[ASN][1000 genomes]
rs28418378	0.82[ASN][1000 genomes]
rs28600991	0.87[ASN][1000 genomes]
rs2949626	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949645	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2949646	0.89[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2949647	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2949649	0.92[ASN][1000 genomes]
rs2949651	0.92[ASN][1000 genomes]
rs3018057	0.91[ASN][1000 genomes]
rs3018059	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018060	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3018061	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3018062	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3018063	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3018065	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3018067	0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3109950	0.98[ASN][1000 genomes]
rs3109951	0.98[ASN][1000 genomes]
rs3109952	0.98[ASN][1000 genomes]
rs3109954	0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3109956	0.98[ASN][1000 genomes]
rs3113246	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3113251	0.98[ASN][1000 genomes]
rs3133167	0.96[ASN][1000 genomes]
rs3133172	0.98[ASN][1000 genomes]
rs3133173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34305991	0.95[ASN][1000 genomes]
rs34909190	0.88[ASN][1000 genomes]
rs34923623	0.95[ASN][1000 genomes]
rs4415033	0.95[ASN][1000 genomes]
rs4441824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4533833	0.88[ASN][1000 genomes]
rs4560491	0.94[CHB][hapmap];0.96[ASN][1000 genomes]
rs4582218	0.95[ASN][1000 genomes]
rs57983950	0.95[ASN][1000 genomes]
rs6533241	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6533244	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs6848855	0.96[ASN][1000 genomes]
rs727618	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7442226	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7669347	0.82[ASN][1000 genomes]
rs7677394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7680756	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7694217	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9991203	0.94[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs9993259	0.95[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	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1819960	chr4:107216320-107246136	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3109959	OSTC	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107114600-107236000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:107155600-107236000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:107178000-107236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:107178000-107236200	Weak transcription	Right Ventricle	heart
5	chr4:107178000-107236600	Weak transcription	Esophagus	oesophagus
6	chr4:107178000-107236600	Weak transcription	Pancreas	Pancrea
7	chr4:107178200-107236000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:107198800-107235600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:107202800-107236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:107204000-107235800	Weak transcription	Psoas Muscle	Psoas
11	chr4:107204000-107236200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:107205600-107236000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:107209000-107231200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:107209200-107236000	Weak transcription	HMEC	breast
15	chr4:107212200-107234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:107213200-107235600	Weak transcription	Fetal Kidney	kidney
17	chr4:107213200-107236200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:107213400-107236000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:107213400-107236200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:107215600-107236000	Weak transcription	Brain Germinal Matrix	brain
21	chr4:107215600-107236200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:107215800-107236600	Weak transcription	Small Intestine	intestine
23	chr4:107215800-107236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:107216000-107235600	Weak transcription	Fetal Intestine Small	intestine
25	chr4:107216200-107236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:107216200-107236200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:107216200-107236200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:107216400-107233800	Weak transcription	NH-A	brain
29	chr4:107216400-107235200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:107216400-107236000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:107216400-107236200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:107216400-107236200	Weak transcription	Thymus	Thymus
33	chr4:107216400-107236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:107217800-107236000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:107218800-107236200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:107220200-107235600	Weak transcription	Fetal Brain Male	brain
37	chr4:107221200-107236000	Weak transcription	Placenta	Placenta
38	chr4:107221200-107236000	Weak transcription	HUVEC	blood vessel
39	chr4:107221200-107236600	Weak transcription	Left Ventricle	heart
40	chr4:107221400-107234200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:107221400-107236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:107221400-107236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:107221400-107236200	Weak transcription	Fetal Stomach	stomach
44	chr4:107221800-107236200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:107222000-107234400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:107223400-107231600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:107223600-107233000	Weak transcription	HSMMtube	muscle
48	chr4:107223600-107234400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:107223600-107236000	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:107223600-107236200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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