Variant report

Variant	rs3752689
Chromosome Location	chr2:179312613-179312614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179312587-179314225	GM12878	blood:	n/a	n/a
2	RFX5	chr2:179312546-179312722	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
2	chr2:179312406..179314073-chr2:179314243..179316047,2	K562	blood:
3	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
4	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
5	chr2:179276988..179281129-chr2:179311895..179317764,7	MCF-7	breast:
6	chr2:179311612..179313781-chr2:179328660..179331380,2	K562	blood:

No data

Variant related genes	Relation type
DFNB59	TF binding region
PRKRA	TF binding region
ENSG00000079150	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000223960	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10179153	0.81[ASN][1000 genomes]
rs10207436	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs10930831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12052983	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13382684	0.86[EUR][1000 genomes]
rs13411588	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1559908	1.00[JPT][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1967327	0.95[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1978580	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2016615	0.87[ASN][1000 genomes]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2114582	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2249737	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2288320	0.90[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2288322	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2366603	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2366604	0.83[ASN][1000 genomes]
rs2886712	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769866	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs3813250	0.82[CHB][hapmap]
rs4894017	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs4894018	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4894019	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4894020	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6704545	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710856	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6726043	0.89[ASN][1000 genomes]
rs6739142	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753709	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6758838	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575643	0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589679	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7598228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7600176	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602597	0.86[CEU][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs957875	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs967507	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9967820	1.00[JPT][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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv1841610	chr2:179296271-179312613	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1817469	chr2:179296271-179319391	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv9296	chr2:179308042-179315047	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	esv3458780	chr2:179312167-179315082	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	esv3458779	chr2:179312250-179314994	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	esv3445737	chr2:179312275-179314988	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	esv3458781	chr2:179312298-179314971	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3458782	chr2:179312312-179314972	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3752689	PLEKHA3	cis	Lymphoblastoid	GTEx
rs3752689	ATP2C2	trans	parietal	SCAN
rs3752689	FKBP7	cis	parietal	SCAN
rs3752689	FKBP7	cis	lymphoblastoid	seeQTL
rs3752689	PLEKHA3	cis	lymphoblastoid	seeQTL
rs3752689	PRKRA	cis	lymphoblastoid	seeQTL
rs3752689	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs3752689	PRKRA	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179279800-179313800	Weak transcription	Stomach Mucosa	stomach
2	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:179290200-179312800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:179291000-179313200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:179291000-179313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:179291000-179313600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:179291200-179312800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:179291200-179312800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:179291200-179312800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:179291200-179313600	Strong transcription	Fetal Thymus	thymus
11	chr2:179291200-179313800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:179291400-179312800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:179291400-179313400	Strong transcription	HSMM	muscle
14	chr2:179291400-179313600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:179291600-179312800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:179291600-179312800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:179291600-179313200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:179291600-179313400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:179291600-179313600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:179291800-179313000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:179291800-179314000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:179292000-179314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:179292400-179312800	Weak transcription	Fetal Heart	heart
24	chr2:179293600-179313000	Strong transcription	Liver	Liver
25	chr2:179293800-179313600	Strong transcription	Adipose Nuclei	Adipose
26	chr2:179293800-179313800	Strong transcription	HUVEC	blood vessel
27	chr2:179294000-179313000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:179294200-179314200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:179295400-179312800	Strong transcription	HepG2	liver
30	chr2:179295400-179313600	Strong transcription	Fetal Intestine Large	intestine
31	chr2:179295400-179314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:179297000-179313200	Weak transcription	Right Atrium	heart
33	chr2:179298600-179314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:179299600-179314800	Weak transcription	Small Intestine	intestine
35	chr2:179302000-179313400	Strong transcription	NHDF-Ad	bronchial
36	chr2:179302600-179313000	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:179303200-179313800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:179303200-179313800	Strong transcription	NH-A	brain
39	chr2:179304000-179314200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:179304400-179313400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:179304400-179314000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:179304600-179313600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr2:179304600-179314000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:179304600-179314000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:179304800-179313200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:179304800-179313200	Strong transcription	K562	blood
47	chr2:179304800-179314000	Strong transcription	A549	lung
48	chr2:179305000-179312800	Strong transcription	Fetal Kidney	kidney
49	chr2:179305000-179313000	Strong transcription	Brain Anterior Caudate	brain
50	chr2:179305000-179313800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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