Variant report

Variant	rs712530
Chromosome Location	chr3:113015956-113015957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:113015910-113015960	AoSMC	blood vessel:	n/a
2	chr3:113015910-113015960	HNPCEpiC	eye:	n/a
3	chr3:113015910-113015960	SAEC	small airway:	n/a
4	chr3:113015910-113015960	MCF10A-Er-Src	breast:	n/a
5	chr3:113015910-113015960	AG09319	gingival:	n/a
6	chr3:113015910-113015960	H1-hESC	embryonic stem cell:	embryo
7	chr3:113015910-113015960	HIPEpiC	eye:	n/a
8	chr3:113015910-113015960	HCM	heart:	n/a
9	chr3:113015910-113015960	LNCaP	prostate:	n/a
10	chr3:113015910-113015960	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:113015910-113015960	PANC-1	pancreas:	n/a
12	chr3:113015910-113015960	HL-60	blood:	n/a
13	chr3:113015910-113015960	CMK	blood:	n/a
14	chr3:113015910-113015960	ECC-1	luminal epithelium:	n/a
15	chr3:113015910-113015960	BJ	skin:	n/a
16	chr3:113015910-113015960	ProgFib	skin:	n/a
17	chr3:113015910-113015960	HCPEpiC	choroid plexus:	n/a
18	chr3:113015910-113015960	GM12891	blood:	n/a
19	chr3:113015910-113015960	NB4	blood:	n/a
20	chr3:113015910-113015960	AG04449	skin:	fetal
21	chr3:113015910-113015960	K562	blood:	n/a
22	chr3:113015910-113015960	HCF	heart:	n/a
23	chr3:113015910-113015960	HCT-116	colon:	n/a
24	chr3:113015910-113015960	HEEpiC	esophagus:	n/a
25	chr3:113015910-113015960	Caco-2	colon:	n/a
26	chr3:113015910-113015960	NHDF-neo	bronchial:	n/a
27	chr3:113015910-113015960	BE2_C	brain:	n/a
28	chr3:113015910-113015960	HRE	kidney:	n/a
29	chr3:113015910-113015960	Hela-S3	cervix:	n/a
30	chr3:113015910-113015960	RPTEC	kidney:	n/a
31	chr3:113015910-113015960	T-47D	breast:	n/a
32	chr3:113015910-113015960	IMR90	lung:	fetal
33	chr3:113015910-113015960	SK-N-MC	brain:	n/a
34	chr3:113015910-113015960	NHBE	bronchial:	n/a
35	chr3:113015910-113015960	GM12892	blood:	n/a
36	chr3:113015910-113015960	SK-N-SH_RA	brain:	n/a
37	chr3:113015910-113015960	U87	brain:	n/a
38	chr3:113015910-113015960	HUVEC	blood vessel:	n/a
39	chr3:113015910-113015960	GM12878	blood:	n/a
40	chr3:113015910-113015960	HepG2	liver:	n/a
41	chr3:113015910-113015960	NT2-D1	testis:	n/a
42	chr3:113015910-113015960	ovcar-3	ovarian:	n/a
43	chr3:113015910-113015960	SK-N-SH	brain:	n/a
44	chr3:113015910-113015960	GM06990	blood:	n/a
45	chr3:113015910-113015960	HEK293	kidney:	embryo
46	chr3:113015910-113015960	HMEC	breast:	n/a
47	chr3:113015910-113015960	MCF-7	breast:	n/a
48	chr3:113015910-113015960	NH-A	brain:	n/a
49	chr3:113015910-113015960	HRCEpiC	kidney:	n/a
50	chr3:113015910-113015960	AG09309	skin:	n/a

No data

Variant related genes	Relation type
WDR52	CpG island

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

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

rs_ID	r²[population]
rs1082588	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1082589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330209	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12330211	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1471883	0.94[CEU][hapmap]
rs1471884	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs2270782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270783	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270785	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291905	0.81[GIH][hapmap];0.94[TSI][hapmap]
rs2936812	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4396864	0.89[CEU][hapmap]
rs6438137	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769604	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs6783479	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793192	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801402	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805535	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618847	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637618	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs775214	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775215	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775217	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs810209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852703	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712530	BOC	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
4	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
7	chr3:112995400-113035800	Weak transcription	Lung	lung
8	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
9	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
10	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
13	chr3:112998600-113036000	Weak transcription	Gastric	stomach
14	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
17	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
18	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:113004600-113016200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
23	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
24	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
25	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
26	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
27	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:113007000-113016400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:113007000-113022600	Weak transcription	Liver	Liver
31	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:113007000-113034400	Weak transcription	HSMM	muscle
35	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:113008000-113023600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
39	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:113008800-113016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:113008800-113016000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
43	chr3:113010800-113022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:113010800-113022600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:113010800-113031000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:113010800-113031400	Weak transcription	Fetal Stomach	stomach
47	chr3:113010800-113034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:113010800-113034400	Weak transcription	Fetal Lung	lung
49	chr3:113010800-113035800	Weak transcription	Ovary	ovary
50	chr3:113011000-113036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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