Variant report

Variant	rs3103091
Chromosome Location	chr4:8538981-8538982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8538338..8543611-chr4:8548493..8553766,7	MCF-7	breast:
2	chr4:8534354..8538693-chr4:8538746..8544060,9	MCF-7	breast:
3	chr4:8537532..8539229-chr4:8550769..8552595,2	MCF-7	breast:
4	chr4:8531043..8532660-chr4:8536787..8539068,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3115401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3115407	0.92[ASN][1000 genomes]
rs34829752	0.95[ASN][1000 genomes]
rs4696887	0.94[AMR][1000 genomes]
rs4696888	0.94[AMR][1000 genomes]
rs6850810	0.92[ASW][hapmap]
rs7435632	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv461221	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv593640	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv980117	chr4:8535043-8545141	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3103091	KIAA0232	cis	cerebellum	SCAN
rs3103091	C4orf23	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8532600-8542800	Enhancers	Placenta	Placenta
2	chr4:8533200-8542800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:8535000-8541600	Enhancers	Pancreas	Pancrea
4	chr4:8535800-8540400	Enhancers	Lung	lung
5	chr4:8536000-8541400	Enhancers	Stomach Mucosa	stomach
6	chr4:8536600-8541400	Enhancers	Esophagus	oesophagus
7	chr4:8536800-8539600	Enhancers	Fetal Thymus	thymus
8	chr4:8537400-8539800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr4:8537400-8542200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:8537600-8542600	Enhancers	GM12878-XiMat	blood
11	chr4:8537800-8539200	Enhancers	Fetal Muscle Leg	muscle
12	chr4:8538000-8539000	Weak transcription	Fetal Kidney	kidney
13	chr4:8538200-8539400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:8538200-8541600	Enhancers	HMEC	breast
15	chr4:8538200-8542200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:8538200-8542200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:8538400-8539000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:8538400-8539200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr4:8538400-8539200	Enhancers	Rectal Smooth Muscle	rectum
20	chr4:8538400-8539400	Enhancers	HSMMtube	muscle
21	chr4:8538400-8541200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:8538400-8541200	Enhancers	Osteobl	bone
23	chr4:8538400-8542200	Enhancers	NHDF-Ad	bronchial
24	chr4:8538600-8539000	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr4:8538600-8539000	Enhancers	Fetal Intestine Large	intestine
26	chr4:8538600-8539000	Enhancers	Spleen	Spleen
27	chr4:8538600-8539200	Enhancers	Fetal Stomach	stomach
28	chr4:8538600-8539200	Enhancers	HUVEC	blood vessel
29	chr4:8538600-8539400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:8538600-8539400	Enhancers	Fetal Lung	lung
31	chr4:8538600-8539400	Enhancers	Ovary	ovary
32	chr4:8538600-8539600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:8538600-8539600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:8538600-8539600	Enhancers	Gastric	stomach
35	chr4:8538600-8539600	Enhancers	NHEK	skin
36	chr4:8538600-8539800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:8538600-8541200	Enhancers	HSMM	muscle
38	chr4:8538600-8541200	Enhancers	NHLF	lung
39	chr4:8538600-8542200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:8538800-8539000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:8538800-8539000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:8538800-8539000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:8538800-8539000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr4:8538800-8539000	Active TSS	Hela-S3	cervix
45	chr4:8538800-8539200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:8538800-8539200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:8538800-8539200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:8538800-8539200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr4:8538800-8539200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr4:8538800-8539200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links