Variant report

Variant	rs17049968
Chromosome Location	chr4:120159916-120159917
allele	A/G
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	ATF2	chr4:120158972-120159927	GM12878	blood:	n/a	n/a
2	MTA3	chr4:120159045-120159946	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120132950..120135145-chr4:120157017..120160702,4	MCF-7	breast:
2	chr4:120158506..120160403-chr4:120160643..120163574,2	MCF-7	breast:

Variant related genes	Relation type
USP53	TF binding region
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10518301	0.93[CHD][hapmap]
rs11935130	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12644283	0.85[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap]
rs12645079	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12645965	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12647635	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12649811	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650267	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17642800	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858285	0.93[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2102541	0.86[CHD][hapmap];0.83[GIH][hapmap];0.85[MKK][hapmap]
rs28421394	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28848291	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28864107	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35372126	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833614	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4834762	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs4834768	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4834769	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55732167	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56072232	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56344202	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62328369	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62328371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328372	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62328376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328377	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328379	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328398	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328407	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7668423	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv966480	chr4:120144708-120160847	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv461632	chr4:120158734-120180790	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv461633	chr4:120158734-120180790	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv595332	chr4:120158734-120180790	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17049968	FABP2	cis	cerebellum	SCAN
rs17049968	FABP2	cis	Whole Blood	GTEx
rs17049968	FABP2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
9	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:120139400-120165800	Weak transcription	Fetal Kidney	kidney
11	chr4:120140600-120167400	Weak transcription	Colonic Mucosa	Colon
12	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
13	chr4:120143000-120167200	Weak transcription	Placenta	Placenta
14	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
15	chr4:120143800-120167000	Weak transcription	Fetal Intestine Large	intestine
16	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:120152200-120167200	Weak transcription	Pancreas	Pancrea
19	chr4:120153800-120160600	Weak transcription	HSMM	muscle
20	chr4:120154800-120161800	Weak transcription	A549	lung
21	chr4:120155000-120166200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:120155200-120161000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:120155200-120163400	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:120155200-120167000	Weak transcription	NH-A	brain
25	chr4:120155400-120160600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:120155400-120160600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:120155400-120165200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:120155400-120165800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:120155400-120166400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:120155400-120167200	Weak transcription	Aorta	Aorta
31	chr4:120155400-120167200	Weak transcription	Fetal Thymus	thymus
32	chr4:120155400-120167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:120155400-120169800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:120155400-120169800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:120155400-120169800	Weak transcription	Ovary	ovary
36	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
38	chr4:120155600-120165800	Weak transcription	HSMMtube	muscle
39	chr4:120155600-120169800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
42	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
43	chr4:120155800-120163800	Strong transcription	NHDF-Ad	bronchial
44	chr4:120156200-120162400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:120156200-120165200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:120156200-120167200	Weak transcription	Psoas Muscle	Psoas
47	chr4:120156600-120163000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:120156800-120167200	Weak transcription	Fetal Intestine Small	intestine
49	chr4:120156800-120167200	Weak transcription	Fetal Stomach	stomach
50	chr4:120157000-120170000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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