Variant report

Variant	rs1983235
Chromosome Location	chr3:141049964-141049965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:141043965..141046482-chr3:141049207..141051849,3	K562	blood:
2	chr3:141030424..141032274-chr3:141049079..141051494,2	MCF-7	breast:
3	chr3:141047658..141052071-chr3:141085661..141088836,5	K562	blood:
4	chr3:141047400..141052083-chr3:141058382..141063565,6	K562	blood:
5	chr3:141021600..141024263-chr3:141049784..141051636,2	MCF-7	breast:
6	chr3:141044721..141047194-chr3:141049083..141050797,2	MCF-7	breast:
7	chr3:141049312..141052024-chr3:141065139..141067701,2	K562	blood:
8	chr3:141030385..141032264-chr3:141049679..141051304,2	K562	blood:
9	chr3:141040944..141042691-chr3:141048357..141050949,3	K562	blood:
10	chr3:141035261..141038228-chr3:141049872..141051864,2	MCF-7	breast:
11	chr3:141048273..141051741-chr3:141060770..141063565,3	K562	blood:
12	chr3:141049236..141052063-chr3:141085767..141088852,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1511380	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs1983234	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4325905	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs59539710	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771916	0.85[AMR][1000 genomes]
rs6777886	0.96[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6795197	0.96[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795377	0.96[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7616781	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs7636469	0.96[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829470	0.88[YRI][hapmap]
rs9843461	0.96[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141045800-141050000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:141045800-141050200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:141045800-141051200	Weak transcription	Lung	lung
4	chr3:141046000-141053800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:141046200-141053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:141046200-141055800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:141046400-141052400	Weak transcription	Pancreas	Pancrea
8	chr3:141046400-141055800	Genic enhancers	Fetal Intestine Small	intestine
9	chr3:141047000-141055800	Genic enhancers	Fetal Intestine Large	intestine
10	chr3:141047600-141050200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:141047600-141054200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:141047800-141050000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:141047800-141050200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:141047800-141050200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:141047800-141050200	Weak transcription	Right Atrium	heart
16	chr3:141047800-141051200	Weak transcription	Colonic Mucosa	Colon
17	chr3:141047800-141051200	Weak transcription	Left Ventricle	heart
18	chr3:141048000-141051400	Weak transcription	Right Ventricle	heart
19	chr3:141048800-141050200	Enhancers	K562	blood
20	chr3:141049000-141050200	Enhancers	Hela-S3	cervix
21	chr3:141049000-141050200	Enhancers	NHDF-Ad	bronchial
22	chr3:141049000-141052400	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:141049000-141052600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:141049000-141052600	Enhancers	Small Intestine	intestine
25	chr3:141049000-141052800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:141049000-141053200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:141049000-141056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:141049200-141050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:141049200-141050200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:141049200-141050200	Enhancers	A549	lung
31	chr3:141049200-141052000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:141049200-141052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:141049200-141055000	Enhancers	GM12878-XiMat	blood
34	chr3:141049200-141057000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:141049400-141052200	Enhancers	HUVEC	blood vessel
36	chr3:141049400-141053200	Enhancers	NH-A	brain
37	chr3:141049400-141053400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:141049400-141056800	Enhancers	NHLF	lung
39	chr3:141049600-141050000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:141049600-141051400	Enhancers	Osteobl	bone
41	chr3:141049600-141051800	Enhancers	HSMMtube	muscle
42	chr3:141049600-141053200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:141049800-141050600	Enhancers	HepG2	liver

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