Variant report

Variant	rs3109958
Chromosome Location	chr4:107233188-107233189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10003024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10016884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10017969	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10018910	0.96[ASN][1000 genomes]
rs10027207	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10049933	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732251	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732791	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11932523	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12642691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650692	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13101612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13114479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13138528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17272618	0.96[ASN][1000 genomes]
rs2691804	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28467469	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28784652	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28805707	0.95[ASN][1000 genomes]
rs28845843	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949625	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2949650	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3018066	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3018069	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3109953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3113250	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133169	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4307042	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314353	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4374692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4382109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4508971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4569824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533242	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6836198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844105	0.96[ASN][1000 genomes]
rs6849573	0.96[ASN][1000 genomes]
rs6852388	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7340989	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7438546	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7668276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7689298	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7692652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs7693333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7693448	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3109958	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs3109958	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:107209200-107236000	Weak transcription	HMEC	breast
14	chr4:107212200-107234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:107213200-107235600	Weak transcription	Fetal Kidney	kidney
16	chr4:107213200-107236200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:107213400-107236000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:107213400-107236200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:107215600-107236000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:107215600-107236200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:107215800-107236600	Weak transcription	Small Intestine	intestine
22	chr4:107215800-107236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:107216000-107235600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:107216200-107236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:107216200-107236200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:107216200-107236200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:107216400-107233800	Weak transcription	NH-A	brain
28	chr4:107216400-107235200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:107216400-107236000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:107216400-107236200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:107216400-107236200	Weak transcription	Thymus	Thymus
32	chr4:107216400-107236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:107217800-107236000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:107218800-107236200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:107220200-107235600	Weak transcription	Fetal Brain Male	brain
36	chr4:107221200-107236000	Weak transcription	Placenta	Placenta
37	chr4:107221200-107236000	Weak transcription	HUVEC	blood vessel
38	chr4:107221200-107236600	Weak transcription	Left Ventricle	heart
39	chr4:107221400-107234200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:107221400-107236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:107221400-107236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:107221400-107236200	Weak transcription	Fetal Stomach	stomach
43	chr4:107221800-107236200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:107222000-107234400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:107223600-107234400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:107223600-107236000	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:107223600-107236200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:107223600-107236200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:107224000-107236200	Weak transcription	Stomach Mucosa	stomach
50	chr4:107224000-107236400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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