Variant report

Variant	rs3779536
Chromosome Location	chr7:127233977-127233978
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:127233910-127234129	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr7:127233718-127234308	K562	blood:	n/a	n/a
3	POLR2A	chr7:127233895-127234200	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:127232638-127235426	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr7:127233507-127234138	K562	blood:	n/a	n/a
6	POLR2A	chr7:127233736-127234386	GM12891	blood:	n/a	n/a
7	POLR2A	chr7:127233915-127234036	K562	blood:	n/a	n/a
8	POLR2A	chr7:127233551-127234137	GM12891	blood:	n/a	n/a
9	POLR2A	chr7:127233815-127234175	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:127232444-127234468	MCF10A-Er-Src	breast:	n/a	n/a
11	RFX5	chr7:127233879-127234232	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:127233721-127234283	GM12892	blood:	n/a	n/a
13	POLR2A	chr7:127233823-127234168	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr7:127233475-127234164	K562	blood:	n/a	n/a
15	POLR2A	chr7:127233866-127234066	MCF-7	breast:	n/a	n/a
16	POLR2A	chr7:127233675-127234116	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr7:127233526-127234164	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:127233727-127234357	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127232149..127233978-chr7:127290816..127293700,2	MCF-7	breast:
2	chr7:127224949..127227429-chr7:127232952..127234995,2	MCF-7	breast:
3	chr7:127232542..127235287-chr7:127252972..127255661,2	K562	blood:
4	chr7:127227908..127231054-chr7:127231482..127236620,11	MCF-7	breast:
5	chr7:127232880..127234701-chr7:127291672..127293969,3	K562	blood:

No data

Variant related genes	Relation type
FSCN3	TF binding region
GCC1	TF binding region
ENSG00000197157	Chromatin interaction
ENSG00000240790	Chromatin interaction
ENSG00000106331	Chromatin interaction
ENSG00000004059	Chromatin interaction
ENSG00000179562	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11973012	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs11976330	0.89[CHB][hapmap]
rs3735640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3757790	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757791	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757792	0.82[ASN][1000 genomes]
rs55889918	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56910747	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60535548	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73720857	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7778682	0.90[CHB][hapmap]
rs7799837	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3779536	NUFIP2	trans	brain	seeQTL
rs3779536	POU3F2	trans	brain	seeQTL
rs3779536	KRCC1	trans	brain	seeQTL
rs3779536	SLC5A3	trans	brain	seeQTL
rs3779536	MPHOSPH10	trans	brain	seeQTL
rs3779536	ZNF830	trans	brain	seeQTL
rs3779536	PHACTR1	trans	brain	seeQTL
rs3779536	ESF1	trans	brain	seeQTL
rs3779536	DDX6	trans	brain	seeQTL
rs3779536	CBX5	trans	brain	seeQTL
rs3779536	SUGT1	trans	brain	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127229600-127241000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:127229800-127234000	Strong transcription	Fetal Brain Female	brain
3	chr7:127229800-127237400	Weak transcription	Right Atrium	heart
4	chr7:127230000-127234000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:127230000-127234000	Strong transcription	Fetal Stomach	stomach
6	chr7:127230000-127234400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:127230200-127234000	Weak transcription	Fetal Brain Male	brain
8	chr7:127231400-127234600	Weak transcription	A549	lung
9	chr7:127231400-127234600	Weak transcription	GM12878-XiMat	blood
10	chr7:127231400-127234600	Weak transcription	HepG2	liver
11	chr7:127231600-127235200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:127231600-127237000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:127231600-127241000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:127232000-127234000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:127232000-127234000	Weak transcription	Lung	lung
16	chr7:127232000-127234400	Weak transcription	Esophagus	oesophagus
17	chr7:127232000-127234600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:127232000-127235000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:127232000-127235000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:127232000-127235000	Weak transcription	HUVEC	blood vessel
21	chr7:127232000-127235200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:127232000-127235200	Weak transcription	Gastric	stomach
23	chr7:127232000-127235400	Weak transcription	NHLF	lung
24	chr7:127232000-127235600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:127232000-127235800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:127232000-127238200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:127232000-127240600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:127232000-127240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:127232000-127240800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:127232000-127243200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:127232000-127245600	Weak transcription	Aorta	Aorta
32	chr7:127232200-127234000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:127232200-127234000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:127232200-127234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:127232200-127234000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:127232200-127234000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:127232200-127234000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:127232200-127234000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:127232200-127234000	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:127232200-127234000	Weak transcription	Brain Substantia Nigra	brain
41	chr7:127232200-127234000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:127232200-127234000	Weak transcription	Fetal Lung	lung
43	chr7:127232200-127234000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:127232200-127234000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:127232200-127234000	Weak transcription	HMEC	breast
46	chr7:127232200-127234000	Weak transcription	NHEK	skin
47	chr7:127232200-127234200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:127232200-127234200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:127232200-127234200	Weak transcription	Osteobl	bone
50	chr7:127232200-127234400	Weak transcription	Primary T cells fromperipheralblood	blood

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