Variant report

Variant	rs3113249
Chromosome Location	chr4:107239130-107239131
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:107236575-107239230	IMR90	lung:	n/a	n/a
2	POLR2A	chr4:107236164-107239299	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:107238957-107239204	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:107236078-107240087	K562	blood:	n/a	n/a
5	POLR2A	chr4:107238927-107239364	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:107236150-107239192	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:107236165-107239379	IMR90	lung:	n/a	n/a
8	POLR2A	chr4:107238816-107239285	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:107236059-107239397	HepG2	liver:	n/a	n/a
10	HEY1	chr4:107236097-107239161	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:107236519-107239214	GM18505	blood:	n/a	n/a
12	HEY1	chr4:107235975-107239381	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:107236175-107239319	GM12891	blood:	n/a	n/a
14	POLR2A	chr4:107236155-107239882	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:107238766..107241197-chr4:107243663..107246436,3	MCF-7	breast:

Variant related genes	Relation type
TBCK	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10003024	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10008428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10017969	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10018910	0.95[ASN][1000 genomes]
rs10027207	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10049933	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732791	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12642691	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13101612	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	0.95[ASN][1000 genomes]
rs2691804	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28467469	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28784652	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28805707	0.94[ASN][1000 genomes]
rs28845843	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2949625	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949650	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3018066	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3018069	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3109953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109955	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109958	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]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113250	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133169	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4307042	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314353	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4374692	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508971	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4569824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533242	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844105	0.95[ASN][1000 genomes]
rs6849573	0.95[ASN][1000 genomes]
rs6852388	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7663321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	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]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7689298	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7692652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs7693333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7693448	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9991203	0.84[ASW][hapmap]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3113249	ELOVL6	cis	cerebellum	SCAN
rs3113249	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs3113249	TBCK	cis	parietal	SCAN
rs3113249	TBCK	cis	lymphoblastoid	seeQTL
rs3113249	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107235600-107239400	Active TSS	A549	lung
2	chr4:107236200-107240000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:107236400-107239200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:107236400-107239400	Active TSS	Colonic Mucosa	Colon
5	chr4:107238000-107239400	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr4:107238000-107239400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:107238200-107239200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:107238200-107239200	Flanking Active TSS	Fetal Lung	lung
9	chr4:107238200-107239200	Flanking Active TSS	HMEC	breast
10	chr4:107238200-107239400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr4:107238200-107239400	Flanking Active TSS	Liver	Liver
12	chr4:107238200-107239600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr4:107238200-107240000	Flanking Active TSS	Osteobl	bone
14	chr4:107238200-107240800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:107238400-107239200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr4:107238400-107239200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr4:107238400-107239200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:107238400-107239200	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr4:107238400-107239200	Flanking Active TSS	Hela-S3	cervix
20	chr4:107238400-107239200	Flanking Active TSS	HUVEC	blood vessel
21	chr4:107238400-107239200	Flanking Active TSS	NHEK	skin
22	chr4:107238400-107239400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:107238400-107239400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr4:107238400-107239400	Flanking Active TSS	NHDF-Ad	bronchial
25	chr4:107238400-107239600	Active TSS	HepG2	liver
26	chr4:107238400-107240000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:107238400-107240000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:107238400-107240000	Flanking Active TSS	Dnd41	blood
29	chr4:107238400-107240600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:107238600-107239200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:107238600-107239200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:107238600-107239200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:107238600-107239200	Enhancers	Fetal Heart	heart
34	chr4:107238600-107239200	Flanking Active TSS	Fetal Kidney	kidney
35	chr4:107238600-107239200	Enhancers	Small Intestine	intestine
36	chr4:107238600-107239200	Flanking Active TSS	NH-A	brain
37	chr4:107238600-107239400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:107238600-107239400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr4:107238600-107239400	Enhancers	Primary B cells from peripheral blood	blood
40	chr4:107238600-107239400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr4:107238600-107239400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr4:107238600-107239800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:107238600-107240000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:107238600-107241800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:107238600-107241800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:107238600-107241800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:107238600-107241800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:107238600-107241800	Weak transcription	Left Ventricle	heart
49	chr4:107238600-107241800	Weak transcription	Lung	lung
50	chr4:107238600-107242000	Weak transcription	Esophagus	oesophagus

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