Variant report

Variant	rs7677572
Chromosome Location	chr4:166299579-166299580
allele	C/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	REST	chr4:166299004-166301874	H1-neurons	neurons:	n/a	chr4:166300166-166300179 chr4:166299047-166299055 chr4:166300164-166300182
2	MXI1	chr4:166299094-166301418	SK-N-SH	brain:	n/a	n/a
3	REST	chr4:166299527-166300557	H1-neurons	neurons:	n/a	chr4:166300166-166300179 chr4:166300164-166300182
4	JUND	chr4:166299423-166300536	SK-N-SH	brain:	n/a	chr4:166299945-166299956

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:166298064..166301679-chr4:166306197..166309667,4	MCF-7	breast:
2	chr4:166298593..166300612-chr4:166306180..166307966,2	MCF-7	breast:

Variant related genes	Relation type
CPE	TF binding region
ENSG00000207559	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11940090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12506365	1.00[CHD][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13106028	1.00[ASN][1000 genomes]
rs13137171	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2241816	1.00[GIH][hapmap]
rs4690813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4691187	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6536907	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6536908	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6842704	1.00[ASN][1000 genomes]
rs6853552	1.00[JPT][hapmap]
rs7671176	1.00[ASN][1000 genomes]
rs7696111	0.82[ASN][1000 genomes]
rs934814	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7677572	HAVCR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166298000-166302400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:166299000-166299600	Enhancers	Fetal Intestine Large	intestine
3	chr4:166299000-166299800	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr4:166299000-166299800	Flanking Active TSS	Fetal Brain Female	brain
5	chr4:166299000-166300000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:166299200-166299600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:166299200-166299600	Flanking Active TSS	Fetal Brain Male	brain
8	chr4:166299200-166299600	Enhancers	Fetal Intestine Small	intestine
9	chr4:166299200-166299600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:166299200-166299600	Enhancers	Fetal Stomach	stomach
11	chr4:166299200-166299800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:166299200-166299800	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:166299200-166300000	Flanking Active TSS	HepG2	liver
14	chr4:166299200-166301000	Active TSS	Colon Smooth Muscle	Colon
15	chr4:166299200-166301400	Active TSS	Rectal Smooth Muscle	rectum
16	chr4:166299200-166303200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:166299400-166299600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
18	chr4:166299400-166299600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr4:166299400-166299600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr4:166299400-166299600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:166299400-166299600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:166299400-166299600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:166299400-166299600	Bivalent Enhancer	Fetal Heart	heart
24	chr4:166299400-166299600	Flanking Active TSS	Fetal Kidney	kidney
25	chr4:166299400-166299600	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr4:166299400-166299600	Enhancers	HMEC	breast
27	chr4:166299400-166299800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:166299400-166299800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:166299400-166299800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
30	chr4:166299400-166299800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr4:166299400-166299800	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr4:166299400-166299800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
33	chr4:166299400-166300000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:166299400-166300000	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr4:166299400-166300000	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr4:166299400-166301000	Active TSS	Brain Germinal Matrix	brain
37	chr4:166299400-166301400	Active TSS	Stomach Smooth Muscle	stomach
38	chr4:166299400-166302200	Active TSS	Aorta	Aorta
39	chr4:166299400-166304000	Active TSS	Brain Hippocampus Middle	brain

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