Variant report

Variant	rs3103082
Chromosome Location	chr4:8536360-8536361
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8527606..8529161-chr4:8536192..8537693,2	MCF-7	breast:
2	chr4:8521151..8523574-chr4:8535830..8537925,2	MCF-7	breast:
3	chr4:8534354..8538693-chr4:8538746..8544060,9	MCF-7	breast:
4	chr4:8535864..8537447-chr4:8555763..8557535,2	MCF-7	breast:
5	chr4:8495654..8498484-chr4:8534530..8537327,2	MCF-7	breast:
6	chr4:8535273..8538017-chr4:8547280..8549775,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13140128	0.94[ASN][1000 genomes]
rs16842480	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs16842483	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs16842486	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs16842498	0.94[ASN][1000 genomes]
rs16842557	0.92[ASN][1000 genomes]
rs16842560	0.91[ASN][1000 genomes]
rs16842563	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs16842567	0.87[CHB][hapmap]
rs4247232	0.96[ASN][1000 genomes]
rs4247233	0.94[ASN][1000 genomes]
rs4259044	1.00[ASN][1000 genomes]
rs4358384	1.00[ASN][1000 genomes]
rs4619877	0.92[ASN][1000 genomes]
rs4696692	0.96[ASN][1000 genomes]
rs4696693	0.96[ASN][1000 genomes]
rs4696695	0.96[ASN][1000 genomes]
rs4696696	0.95[ASN][1000 genomes]
rs4696838	0.94[ASN][1000 genomes]
rs55765509	0.96[ASN][1000 genomes]
rs55789011	0.94[ASN][1000 genomes]
rs55977448	0.92[ASN][1000 genomes]
rs56053534	0.92[ASN][1000 genomes]
rs61258495	0.96[ASN][1000 genomes]
rs62287446	1.00[ASN][1000 genomes]
rs62287455	0.92[ASN][1000 genomes]
rs869600	0.96[ASN][1000 genomes]
rs869602	0.99[ASN][1000 genomes]
rs883607	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][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
rs3103082	C4orf23	cis	parietal	SCAN
rs3103082	C4orf23	cis	cerebellum	SCAN

Chromatin state (count:52 , 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	chr4:8533600-8537400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr4:8533800-8537800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:8534800-8536800	Weak transcription	Fetal Thymus	thymus
6	chr4:8535000-8536600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:8535000-8537000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:8535000-8537200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:8535000-8541600	Enhancers	Pancreas	Pancrea
10	chr4:8535200-8536600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:8535200-8536800	Enhancers	Fetal Intestine Small	intestine
12	chr4:8535200-8537400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr4:8535200-8537400	Enhancers	Fetal Intestine Large	intestine
14	chr4:8535200-8538600	Enhancers	Colon Smooth Muscle	Colon
15	chr4:8535400-8536800	Enhancers	HMEC	breast
16	chr4:8535600-8536600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:8535600-8536600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:8535600-8536600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr4:8535600-8536600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:8535600-8536600	Enhancers	HSMMtube	muscle
21	chr4:8535600-8536800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:8535600-8536800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:8535600-8538000	Enhancers	Fetal Kidney	kidney
24	chr4:8535800-8536400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr4:8535800-8536400	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr4:8535800-8536400	Enhancers	NHDF-Ad	bronchial
27	chr4:8535800-8536600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:8535800-8536600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:8535800-8540400	Enhancers	Lung	lung
30	chr4:8536000-8536400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:8536000-8536800	Enhancers	Small Intestine	intestine
32	chr4:8536000-8537200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:8536000-8537200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:8536000-8537800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:8536000-8538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:8536000-8538600	Weak transcription	Fetal Lung	lung
37	chr4:8536000-8538600	Weak transcription	Fetal Stomach	stomach
38	chr4:8536000-8538600	Weak transcription	Gastric	stomach
39	chr4:8536000-8538600	Weak transcription	Ovary	ovary
40	chr4:8536000-8538800	Weak transcription	Colonic Mucosa	Colon
41	chr4:8536000-8541400	Enhancers	Stomach Mucosa	stomach
42	chr4:8536200-8536400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr4:8536200-8536400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:8536200-8536400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:8536200-8536400	Enhancers	Fetal Muscle Leg	muscle
46	chr4:8536200-8536400	Enhancers	Rectal Smooth Muscle	rectum
47	chr4:8536200-8536600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
48	chr4:8536200-8536600	Weak transcription	Esophagus	oesophagus
49	chr4:8536200-8536600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr4:8536200-8536600	Enhancers	NHEK	skin

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