Variant report

Variant	rs1880943
Chromosome Location	chr4:102081357-102081358
allele	C/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	chr4:102081256-102081617	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102072492..102076401-chr4:102080849..102083286,3	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10018021	0.80[EUR][1000 genomes]
rs10030389	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10516471	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13103902	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13111186	0.81[EUR][1000 genomes]
rs13112866	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs13118966	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs13125501	0.82[EUR][1000 genomes]
rs13128841	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13135924	0.81[EUR][1000 genomes]
rs13142024	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1810024	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2063058	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659552	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811063	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs4590038	0.81[EUR][1000 genomes]
rs4698912	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4698913	0.81[EUR][1000 genomes]
rs4699106	0.81[EUR][1000 genomes]
rs7677550	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs950177	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9995338	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv18835	chr4:102081201-102084993	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv2760883	chr4:102081357-102088150	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102075400-102084200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:102078400-102093200	Weak transcription	HUVEC	blood vessel
4	chr4:102078400-102096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:102078600-102088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:102078600-102090200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:102078800-102082000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:102078800-102084000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:102078800-102084000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:102078800-102084000	Weak transcription	HMEC	breast
11	chr4:102078800-102096000	Weak transcription	Ovary	ovary
12	chr4:102079000-102088800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:102079600-102082000	Weak transcription	NHEK	skin
15	chr4:102079600-102088800	Weak transcription	Psoas Muscle	Psoas
16	chr4:102079800-102081400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:102079800-102081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:102079800-102082800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:102079800-102087200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:102079800-102096400	Weak transcription	Adipose Nuclei	Adipose
21	chr4:102080000-102082200	Weak transcription	Brain Substantia Nigra	brain
22	chr4:102080000-102083000	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:102080000-102084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:102080000-102085200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:102080000-102085200	Weak transcription	Osteobl	bone
26	chr4:102080000-102092200	Weak transcription	NHDF-Ad	bronchial
27	chr4:102080000-102092600	Weak transcription	NH-A	brain
28	chr4:102080200-102085200	Weak transcription	HSMM	muscle
29	chr4:102080400-102081600	Weak transcription	Brain Anterior Caudate	brain
30	chr4:102080400-102081600	Enhancers	A549	lung
31	chr4:102080400-102084600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:102080400-102087400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:102080400-102088800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:102080600-102081400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:102080600-102082200	Weak transcription	Brain Angular Gyrus	brain
36	chr4:102080600-102082400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:102080600-102082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:102080600-102093000	Weak transcription	NHLF	lung
39	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:102080800-102082600	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:102081000-102090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:102081200-102082600	Strong transcription	Primary B cells from cord blood	blood

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