Variant report

Variant	rs4677630
Chromosome Location	chr3:191052534-191052535
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:191051764-191053711	PFSK-1	brain:	n/a	n/a
2	MAFK	chr3:191051960-191052556	K562	blood:	n/a	n/a
3	RELA	chr3:191051794-191052835	GM12878	blood:	n/a	n/a
4	RELA	chr3:191051766-191052574	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191049478..191053328-chr3:191074760..191077632,3	K562	blood:
2	chr3:191046891..191049504-chr3:191051045..191053812,2	MCF-7	breast:

Variant related genes	Relation type
UTS2B	TF binding region
ENSG00000188958	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10937477	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1347400	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]
rs1465737	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1473866	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs150506	0.87[ASN][1000 genomes]
rs159488	0.91[ASN][1000 genomes]
rs159489	0.87[ASN][1000 genomes]
rs186066	0.83[CEU][hapmap];0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs188384	0.87[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs188385	0.87[ASN][1000 genomes]
rs192671	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs293797	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs293798	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs293800	0.85[ASN][1000 genomes]
rs293802	0.84[CEU][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs293804	0.85[ASN][1000 genomes]
rs293805	0.81[ASN][1000 genomes]
rs293806	0.85[ASN][1000 genomes]
rs293808	0.87[ASN][1000 genomes]
rs293815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs293844	0.87[ASN][1000 genomes]
rs293846	0.87[ASN][1000 genomes]
rs293851	0.87[ASN][1000 genomes]
rs297396	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs366626	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs367747	0.85[ASN][1000 genomes]
rs368665	0.85[ASN][1000 genomes]
rs369174	0.84[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs373035	0.87[ASN][1000 genomes]
rs381090	0.87[ASN][1000 genomes]
rs383075	0.83[ASN][1000 genomes]
rs390744	0.87[ASN][1000 genomes]
rs401465	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs426466	0.87[ASN][1000 genomes]
rs432085	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs434556	0.85[ASN][1000 genomes]
rs437244	0.85[ASN][1000 genomes]
rs448133	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs448643	1.00[JPT][hapmap]
rs4677628	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs4677734	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4677735	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523270	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs525774	0.87[ASN][1000 genomes]
rs526785	0.87[ASN][1000 genomes]
rs529523	0.87[ASN][1000 genomes]
rs566548	0.84[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6779820	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6953	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs697905	0.85[ASN][1000 genomes]
rs709142	0.87[ASN][1000 genomes]
rs9847278	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4677630	PIGX	cis	cerebellum	SCAN
rs4677630	PPP1R2	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191049000-191058600	Weak transcription	Left Ventricle	heart
2	chr3:191049200-191060600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:191049400-191052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:191049400-191057600	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:191049800-191061600	Weak transcription	HSMMtube	muscle
6	chr3:191050000-191053200	Enhancers	Primary B cells from cord blood	blood
7	chr3:191050000-191053200	Enhancers	K562	blood
8	chr3:191050000-191055600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:191050000-191056400	Weak transcription	Fetal Intestine Small	intestine
10	chr3:191050000-191057200	Weak transcription	Fetal Lung	lung
11	chr3:191050200-191053400	Enhancers	Liver	Liver
12	chr3:191050200-191054400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:191050200-191054800	Enhancers	HepG2	liver
14	chr3:191050200-191055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:191050200-191060200	Weak transcription	Psoas Muscle	Psoas
16	chr3:191050200-191074800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:191050400-191054600	Weak transcription	Osteobl	bone
18	chr3:191050600-191060400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:191050800-191057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:191050800-191057800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:191051000-191052600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:191051000-191053200	Enhancers	Adipose Nuclei	Adipose
23	chr3:191051000-191055400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:191051000-191055400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:191051000-191055800	Weak transcription	HMEC	breast
26	chr3:191051000-191056000	Weak transcription	HSMM	muscle
27	chr3:191051000-191056000	Enhancers	HUVEC	blood vessel
28	chr3:191051200-191060200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:191051400-191053600	Weak transcription	Small Intestine	intestine
30	chr3:191051400-191054600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:191051400-191054600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:191051400-191055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:191051400-191055800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:191051400-191056000	Weak transcription	Fetal Heart	heart
35	chr3:191051400-191056000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:191051400-191057200	Weak transcription	Aorta	Aorta
37	chr3:191051400-191057400	Weak transcription	Ovary	ovary
38	chr3:191051400-191058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:191051400-191059400	Weak transcription	Right Atrium	heart
40	chr3:191051400-191060000	Weak transcription	Brain Germinal Matrix	brain
41	chr3:191051400-191060200	Weak transcription	Brain Anterior Caudate	brain
42	chr3:191051400-191060200	Weak transcription	Right Ventricle	heart
43	chr3:191051600-191054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:191051600-191057000	Weak transcription	Fetal Brain Female	brain
45	chr3:191051800-191053000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:191052000-191052600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:191052000-191052600	Enhancers	Brain Hippocampus Middle	brain
48	chr3:191052000-191052600	Enhancers	NHEK	skin
49	chr3:191052000-191053200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:191052000-191053200	Enhancers	NHLF	lung

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