Variant report

Variant	rs1442490
Chromosome Location	chr4:100326403-100326404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100039211..100039845-chr4:100326145..100326879,2	MCF-7	breast:
2	chr4:100122531..100123516-chr4:100326382..100326915,3	MCF-7	breast:
3	chr4:100038972..100039679-chr4:100326321..100327345,4	K562	blood:
4	chr4:99915893..99916919-chr4:100326329..100327016,3	K562	blood:
5	chr4:100122648..100123636-chr4:100326377..100326984,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1827567	0.86[ASN][1000 genomes]
rs2099855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584462	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284784	0.86[ASN][1000 genomes]
rs284787	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv879659	chr4:100260789-100349135	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv879660	chr4:100284199-100380148	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1847619	chr4:100321443-100430924	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv517344	chr4:100322445-100363569	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv3584518	chr4:100322445-100377763	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3584520	chr4:100324071-100400696	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1442490	ADH5	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100322000-100326800	Enhancers	Fetal Intestine Large	intestine
2	chr4:100322000-100326800	Enhancers	Fetal Intestine Small	intestine
3	chr4:100323000-100327000	Enhancers	Stomach Mucosa	stomach
4	chr4:100323800-100326600	Enhancers	Fetal Kidney	kidney
5	chr4:100323800-100326800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:100323800-100326800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr4:100324000-100326800	Enhancers	Adipose Nuclei	Adipose
8	chr4:100324000-100327200	Enhancers	Small Intestine	intestine
9	chr4:100324200-100327200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:100324400-100326800	Enhancers	NHDF-Ad	bronchial
11	chr4:100324600-100326600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:100324600-100326800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:100324600-100326800	Enhancers	NH-A	brain
14	chr4:100324600-100332400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:100324800-100326800	Enhancers	HSMM	muscle
16	chr4:100325000-100326800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:100325000-100326800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:100325000-100326800	Flanking Active TSS	GM12878-XiMat	blood
19	chr4:100325000-100327000	Enhancers	NHLF	lung
20	chr4:100325200-100326800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:100325200-100326800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:100325200-100326800	Enhancers	HepG2	liver
23	chr4:100325200-100326800	Enhancers	HMEC	breast
24	chr4:100325200-100326800	Enhancers	NHEK	skin
25	chr4:100325200-100327200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:100325400-100326600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr4:100325400-100326800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:100325400-100326800	Flanking Active TSS	Liver	Liver
29	chr4:100325400-100326800	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:100325400-100328800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:100325600-100326800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:100325600-100326800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:100325800-100326800	Enhancers	Pancreas	Pancrea
34	chr4:100325800-100326800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr4:100325800-100326800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr4:100325800-100326800	Enhancers	HSMMtube	muscle
37	chr4:100325800-100326800	Enhancers	HUVEC	blood vessel
38	chr4:100325800-100327000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:100325800-100327200	Enhancers	Ovary	ovary
40	chr4:100326000-100326800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:100326000-100326800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:100326000-100326800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:100326000-100326800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:100326000-100326800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr4:100326000-100327200	Enhancers	Colon Smooth Muscle	Colon
46	chr4:100326000-100334200	Weak transcription	Aorta	Aorta
47	chr4:100326200-100326800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:100326200-100326800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr4:100326200-100326800	Enhancers	Duodenum Mucosa	Duodenum
50	chr4:100326200-100326800	Enhancers	Osteobl	bone

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