Variant report

Variant	rs13151627
Chromosome Location	chr4:174107537-174107538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174105689..174108523-chr4:174110844..174113074,3	K562	blood:
2	chr4:174107501..174109531-chr4:174134790..174137729,2	K562	blood:
3	chr4:174089462..174093511-chr4:174101322..174108928,6	MCF-7	breast:
4	chr4:174105689..174108453-chr4:174111352..174113074,2	K562	blood:
5	chr4:174103017..174104985-chr4:174106308..174108785,2	K562	blood:
6	chr4:174107114..174109913-chr4:174122414..174125175,2	K562	blood:
7	chr4:174102044..174104831-chr4:174106302..174107893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10005325	0.88[EUR][1000 genomes]
rs10471199	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10520255	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520256	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11722807	0.91[JPT][hapmap]
rs11731262	0.83[JPT][hapmap]
rs11734517	0.83[JPT][hapmap]
rs11942280	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13102038	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13116270	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs13117810	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13120215	0.95[EUR][1000 genomes]
rs13123359	0.90[EUR][1000 genomes]
rs13123399	0.85[CEU][hapmap]
rs13124470	0.92[CEU][hapmap]
rs13141844	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs13142524	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13150320	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs1481120	0.82[JPT][hapmap]
rs17059153	0.86[CHB][hapmap]
rs17059154	0.84[CHB][hapmap]
rs17059205	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs17059207	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17059217	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17059235	0.85[CEU][hapmap]
rs1991726	0.85[CEU][hapmap]
rs2332657	0.96[EUR][1000 genomes]
rs2332658	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs28361970	0.91[EUR][1000 genomes]
rs28413646	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28694391	0.81[EUR][1000 genomes]
rs34285915	0.81[EUR][1000 genomes]
rs34718403	0.95[EUR][1000 genomes]
rs35576170	0.87[EUR][1000 genomes]
rs35644315	0.85[EUR][1000 genomes]
rs35679682	0.81[EUR][1000 genomes]
rs35730812	0.84[EUR][1000 genomes]
rs36050097	0.87[EUR][1000 genomes]
rs3775590	0.83[JPT][hapmap]
rs3775591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4380500	0.84[EUR][1000 genomes]
rs4608791	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4695827	0.90[EUR][1000 genomes]
rs4695829	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4696050	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696054	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs61241252	0.80[ASN][1000 genomes]
rs62341096	0.83[EUR][1000 genomes]
rs6553686	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6822924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835517	0.81[CEU][hapmap]
rs6842693	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6858043	0.91[EUR][1000 genomes]
rs722826	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs722827	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7661977	0.95[EUR][1000 genomes]
rs7664847	0.83[JPT][hapmap]
rs7665469	0.92[JPT][hapmap]
rs7667345	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7668435	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7668473	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs7669267	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs7672055	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs7673747	0.91[EUR][1000 genomes]
rs7686909	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs7689781	0.81[CEU][hapmap]
rs934358	0.85[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9685410	0.85[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs9991863	0.96[EUR][1000 genomes]
rs9995556	0.92[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13151627	SCRG1	cis	parietal	SCAN
rs13151627	GALNT7	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
2	chr4:174092800-174109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:174093600-174109800	Weak transcription	Gastric	stomach
4	chr4:174095000-174109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:174096200-174111200	Weak transcription	Small Intestine	intestine
6	chr4:174098800-174108400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:174099000-174109400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:174099200-174111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:174100000-174112200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:174103600-174109400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:174104000-174108000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:174104000-174109400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:174104000-174109400	Weak transcription	Pancreas	Pancrea
14	chr4:174104000-174109400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:174104000-174112400	Weak transcription	Aorta	Aorta
16	chr4:174104000-174112400	Weak transcription	Brain Anterior Caudate	brain
17	chr4:174104000-174112600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:174104000-174157200	Weak transcription	Ovary	ovary
19	chr4:174104200-174108800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:174104200-174112200	Weak transcription	Hela-S3	cervix
21	chr4:174104400-174108600	Weak transcription	Osteobl	bone
22	chr4:174104600-174108600	Weak transcription	NHEK	skin
23	chr4:174104600-174108800	Weak transcription	HMEC	breast
24	chr4:174104600-174108800	Weak transcription	NH-A	brain
25	chr4:174104600-174110000	Weak transcription	HSMMtube	muscle
26	chr4:174104600-174112600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:174105000-174116400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:174105200-174110600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:174105600-174107600	Enhancers	Thymus	Thymus
30	chr4:174105800-174108600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:174105800-174109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:174105800-174109800	Enhancers	Fetal Intestine Small	intestine
33	chr4:174106000-174107800	Enhancers	K562	blood
34	chr4:174106000-174108000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr4:174106000-174108400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr4:174106000-174110200	Enhancers	Fetal Intestine Large	intestine
37	chr4:174106200-174107600	Enhancers	Fetal Thymus	thymus
38	chr4:174106200-174107800	Enhancers	Primary T cells from cord blood	blood
39	chr4:174106200-174107800	Enhancers	Fetal Heart	heart
40	chr4:174106200-174107800	Enhancers	Dnd41	blood
41	chr4:174106200-174108000	Enhancers	HUVEC	blood vessel
42	chr4:174106400-174107600	Enhancers	Primary B cells from peripheral blood	blood
43	chr4:174106400-174107600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr4:174106400-174108000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:174106600-174107600	Enhancers	Primary B cells from cord blood	blood
46	chr4:174106600-174107800	Enhancers	HSMM	muscle
47	chr4:174106600-174108000	Enhancers	Brain Hippocampus Middle	brain
48	chr4:174106600-174114200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:174106800-174107600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr4:174106800-174107800	Enhancers	Primary neutrophils fromperipheralblood	blood

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