Variant report

Variant	rs7596162
Chromosome Location	chr2:11744232-11744233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:11740349-11746570	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11742961..11746645-chr2:11747692..11751157,4	MCF-7	breast:
2	chr2:11742842..11745616-chr2:11746744..11750568,5	MCF-7	breast:
3	chr2:11733968..11736190-chr2:11742659..11745158,2	K562	blood:
4	chr2:11743248..11744961-chr2:11751244..11753907,2	MCF-7	breast:
5	chr2:11737451..11740720-chr2:11742097..11745716,3	MCF-7	breast:
6	chr2:11740125..11742102-chr2:11743265..11746041,3	K562	blood:
7	chr2:11679998..11682711-chr2:11744007..11745638,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000265583	TF binding region
ENSG00000196208	Chromatin interaction
ENSG00000265583	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11681838	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11688915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11689869	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13421972	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs13431704	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13432243	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1435547	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16857679	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1865575	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2252958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2304399	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34592059	0.83[EUR][1000 genomes]
rs36030386	0.80[ASN][1000 genomes]
rs3828298	0.89[CEU][hapmap]
rs4669756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55890755	0.96[EUR][1000 genomes]
rs62118318	0.95[ASN][1000 genomes]
rs6730352	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6735957	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6736604	0.80[ASN][1000 genomes]
rs6744817	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs71446421	0.96[EUR][1000 genomes]
rs7557063	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7559835	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7576944	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs880858	0.80[ASN][1000 genomes]
rs9287733	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7596162	GRHL1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:11733400-11750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:11733600-11750600	Weak transcription	Pancreas	Pancrea
14	chr2:11733600-11784000	Strong transcription	HepG2	liver
15	chr2:11735200-11744600	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr2:11735200-11746400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:11735600-11745000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:11735600-11746600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:11736200-11765000	Weak transcription	Fetal Lung	lung
20	chr2:11736400-11755400	Weak transcription	Brain Substantia Nigra	brain
21	chr2:11736600-11750600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:11736800-11762800	Weak transcription	Fetal Heart	heart
23	chr2:11737000-11744600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:11737600-11744400	Strong transcription	Fetal Stomach	stomach
25	chr2:11737800-11745000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:11737800-11746400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:11738000-11744600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:11738600-11744800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:11739200-11751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:11739200-11752000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:11739600-11744800	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:11739600-11750800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:11740000-11745200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:11740200-11745200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:11741400-11749600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:11741400-11755400	Weak transcription	Liver	Liver
37	chr2:11741600-11749600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:11741600-11750800	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:11742000-11750000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:11742000-11750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:11742200-11749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:11742800-11751000	Strong transcription	Ovary	ovary
43	chr2:11743200-11765200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:11743400-11744600	Strong transcription	Brain Angular Gyrus	brain
45	chr2:11743400-11752600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:11743400-11765000	Weak transcription	Left Ventricle	heart
47	chr2:11743600-11744400	Enhancers	HUVEC	blood vessel
48	chr2:11743800-11744600	Strong transcription	Fetal Kidney	kidney
49	chr2:11743800-11747800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:11743800-11749800	Weak transcription	Brain Anterior Caudate	brain

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