Variant report

Variant	rs1531133
Chromosome Location	chr2:46843631-46843632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:217)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:217 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:46843553-46844696	GM12878	blood:	n/a	n/a
2	YY1	chr2:46843551-46844485	K562	blood:	n/a	n/a
3	ZBTB7A	chr2:46843503-46844244	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr2:46842725-46843851	K562	blood:	n/a	n/a
5	POLR2A	chr2:46843144-46844840	K562	blood:	n/a	n/a
6	POLR2A	chr2:46843457-46844530	K562	blood:	n/a	n/a
7	EBF1	chr2:46843528-46844251	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:46843610-46844725	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:46843058-46844635	GM12878	blood:	n/a	n/a
10	E2F6	chr2:46843437-46844700	A549	lung:	n/a	chr2:46844187-46844196 chr2:46844117-46844129
11	USF2	chr2:46843343-46843647	Hela-S3	cervix:	n/a	n/a
12	MAX	chr2:46843392-46844617	ECC-1	luminal epithelium:	n/a	chr2:46844180-46844189
13	YY1	chr2:46843454-46844526	HepG2	liver:	n/a	n/a
14	TBP	chr2:46843348-46844655	HepG2	liver:	n/a	n/a
15	CREB1	chr2:46843226-46844707	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:46843137-46845416	MCF10A-Er-Src	breast:	n/a	n/a
17	NFIC	chr2:46843230-46844610	HepG2	liver:	n/a	n/a
18	ZNF143	chr2:46843504-46844376	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr2:46843482-46844664	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr2:46843430-46844657	ProgFib	skin:	n/a	n/a
21	SMC3	chr2:46843541-46844489	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr2:46843609-46844701	MCF-7	breast:	n/a	n/a
23	PBX3	chr2:46843577-46844619	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr2:46843494-46844585	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:46843596-46844624	Gliobla	brain:	n/a	n/a
26	MAX	chr2:46843037-46844575	K562	blood:	n/a	chr2:46844180-46844189
27	POLR2A	chr2:46843595-46843867	A549	lung:	n/a	n/a
28	BHLHE40	chr2:46843109-46844466	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:46843195-46844642	A549	lung:	n/a	n/a
30	TCF12	chr2:46843548-46844625	ECC-1	luminal epithelium:	n/a	n/a
31	BCLAF1	chr2:46843552-46844656	GM12878	blood:	n/a	chr2:46844308-46844317
32	E2F6	chr2:46843571-46844479	Hela-S3	cervix:	n/a	chr2:46844187-46844196 chr2:46844117-46844129
33	MAX	chr2:46843501-46844546	H1-hESC	embryonic stem cell:	n/a	chr2:46844180-46844189
34	POLR2A	chr2:46843491-46843633	HUVEC	blood vessel:	n/a	n/a
35	MAX	chr2:46843544-46844598	Hela-S3	cervix:	n/a	chr2:46844180-46844189
36	POLR2A	chr2:46843223-46844594	K562	blood:	n/a	n/a
37	POLR2A	chr2:46843467-46844558	HepG2	liver:	n/a	n/a
38	POLR2A	chr2:46843563-46844576	HepG2	liver:	n/a	n/a
39	MAFK	chr2:46843360-46843665	Hela-S3	cervix:	n/a	n/a
40	TBL1XR1	chr2:46843330-46843955	K562	blood:	n/a	n/a
41	ATF3	chr2:46843451-46844459	A549	lung:	n/a	chr2:46844315-46844329
42	NFIC	chr2:46843328-46844636	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:46843167-46844594	K562	blood:	n/a	n/a
44	POLR2A	chr2:46843402-46844621	HL-60	blood:	n/a	n/a
45	POLR2A	chr2:46843500-46844604	Hela-S3	cervix:	n/a	n/a
46	HDAC2	chr2:46843596-46844580	HepG2	liver:	n/a	n/a
47	MAX	chr2:46842957-46844718	A549	lung:	n/a	chr2:46844180-46844189
48	TAF1	chr2:46843565-46844537	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr2:46843583-46844618	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:46842800-46844614	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:4612398..4613899-chr2:46843451..46845435,2	MCF-7	breast:
2	chr2:46768345..46771564-chr2:46842518..46844841,5	MCF-7	breast:
3	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
4	chr2:46843200..46845178-chr2:47140240..47142665,2	MCF-7	breast:
5	chr2:46806489..46808552-chr2:46842875..46845193,2	MCF-7	breast:
6	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
7	chr2:46838843..46841805-chr2:46843233..46844922,3	MCF-7	breast:
8	chr2:46842180..46843861-chr2:46924432..46926384,2	K562	blood:
9	chr2:46745227..46747707-chr2:46842896..46845007,2	K562	blood:
10	chr2:46839258..46842242-chr2:46842497..46844194,2	K562	blood:
11	chr2:46838114..46840779-chr2:46841900..46844194,2	MCF-7	breast:
12	chr2:46770485..46772962-chr2:46842113..46844264,3	MCF-7	breast:

No data

Variant related genes	Relation type
PIGF	TF binding region
CRIPT	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000141480	Chromatin interaction
ENSG00000171150	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000250116	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1080871	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11894342	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12104572	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001566	0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs13385693	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1451153	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1451156	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1598517	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901263	0.92[CHB][hapmap];0.88[JPT][hapmap];0.92[MKK][hapmap]
rs1989720	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122715	0.86[CHD][hapmap]
rs2242033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305350	0.86[TSI][hapmap]
rs3087822	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544906	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6544907	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739397	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739468	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6752882	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7589801	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7598578	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1531133	CRIPT	cis	Temporal Cortex	GTEx
rs1531133	PIGF	cis	cerebellum	SCAN
rs1531133	CRIPT	cis	parietal	SCAN
rs1531133	CRIPT	cis	Stomach	GTEx
rs1531133	CRIPT	cis	multi-tissue	Pritchard
rs1531133	PIGF	cis	lymphoblastoid	seeQTL
rs1531133	CRIPT	cis	lymphoblastoid	seeQTL
rs1531133	CRIPT	cis	Frontal Cortex	GTEx
rs1531133	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs1531133	PRKCE	cis	cerebellum	SCAN
rs1531133	CRIPT	cis	Lymphoblastoid	GTEx
rs1531133	CRIPT	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46842400-46844000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:46842600-46844000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr2:46842600-46844000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:46842600-46845000	Active TSS	Fetal Intestine Large	intestine
5	chr2:46842600-46845400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:46842600-46845600	Active TSS	Aorta	Aorta
7	chr2:46842800-46843800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:46842800-46843800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr2:46842800-46843800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr2:46842800-46843800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr2:46842800-46844000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr2:46842800-46844000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr2:46842800-46844600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:46842800-46844800	Active TSS	Duodenum Mucosa	Duodenum
15	chr2:46842800-46844800	Active TSS	Fetal Brain Female	brain
16	chr2:46842800-46845000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr2:46842800-46845000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:46842800-46845000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:46842800-46845200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr2:46842800-46845200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:46842800-46845400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr2:46842800-46845400	Active TSS	Right Atrium	heart
23	chr2:46843000-46843800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr2:46843000-46843800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:46843000-46843800	Flanking Active TSS	Thymus	Thymus
26	chr2:46843000-46844000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr2:46843000-46844600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr2:46843000-46844800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:46843000-46844800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:46843000-46844800	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr2:46843000-46844800	Active TSS	Brain Angular Gyrus	brain
32	chr2:46843000-46844800	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:46843000-46844800	Active TSS	Brain Hippocampus Middle	brain
34	chr2:46843000-46844800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr2:46843000-46844800	Active TSS	Pancreas	Pancrea
36	chr2:46843000-46845000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:46843000-46845000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:46843000-46845000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:46843000-46845000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:46843000-46845000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:46843000-46845000	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:46843000-46845000	Active TSS	Fetal Kidney	kidney
43	chr2:46843000-46845000	Active TSS	Fetal Stomach	stomach
44	chr2:46843000-46845000	Active TSS	Right Ventricle	heart
45	chr2:46843000-46845000	Active TSS	NHDF-Ad	bronchial
46	chr2:46843000-46845200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:46843000-46845200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:46843000-46845200	Active TSS	Fetal Intestine Small	intestine
49	chr2:46843000-46845200	Active TSS	GM12878-XiMat	blood
50	chr2:46843000-46845400	Active TSS	HUES48 Cell Line	embryonic stem cell

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