Variant report

Variant	rs6427548
Chromosome Location	chr1:160780965-160780966
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:160780953-160781304	HepG2	liver:	n/a	chr1:160781118-160781133
2	MAFK	chr1:160780951-160781312	HepG2	liver:	n/a	chr1:160781118-160781133
3	MAFF	chr1:160780964-160781302	HepG2	liver:	n/a	chr1:160781116-160781134

No.	Distal block	Cell Line	Cell type
1	chr1:160777120..160779933-chr1:160780615..160783432,4	K562	blood:
2	chr1:160779866..160781807-chr1:160913798..160915545,2	MCF-7	breast:
3	chr1:160776649..160779858-chr1:160780478..160783432,4	K562	blood:
4	chr1:160779738..160781417-chr1:160790589..160793548,2	K562	blood:

Variant related genes	Relation type
LY9	TF binding region
ENSG00000122224	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11265487	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11265489	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2027015	0.93[ASN][1000 genomes]
rs2779800	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs474131	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs485618	0.81[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs492874	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492906	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494091	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs496201	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs504848	0.90[ASN][1000 genomes]
rs505728	0.86[ASN][1000 genomes]
rs506081	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs509749	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs510143	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512645	0.81[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs516509	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs516847	0.88[ASN][1000 genomes]
rs522897	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs539433	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs551827	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs551882	0.91[ASN][1000 genomes]
rs556810	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs567306	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs569659	0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs569911	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs571841	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs574610	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs576334	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs577453	0.89[ASN][1000 genomes]
rs6667581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs790625	0.88[ASN][1000 genomes]
rs790626	0.88[ASN][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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6427548	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs6427548	USF1	cis	lymphoblastoid	seeQTL
rs6427548	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs6427548	CLK2	cis	parietal	SCAN
rs6427548	EFNA3	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160772200-160782000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr1:160774400-160782400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:160775600-160783000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:160777200-160781200	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:160777400-160789000	Strong transcription	Primary B cells from cord blood	blood
7	chr1:160777600-160783400	Weak transcription	Gastric	stomach
8	chr1:160778000-160782800	Weak transcription	GM12878-XiMat	blood
9	chr1:160778000-160783000	Weak transcription	Fetal Thymus	thymus
10	chr1:160778000-160783000	Weak transcription	Thymus	Thymus
11	chr1:160778000-160783800	Weak transcription	Spleen	Spleen
12	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:160778400-160783200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:160778600-160783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:160779600-160781600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:160779800-160781000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:160779800-160781200	Enhancers	Placenta	Placenta
20	chr1:160779800-160789200	Strong transcription	Primary T cells from cord blood	blood
21	chr1:160780000-160781000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:160780000-160781000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:160780000-160781200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:160780000-160781200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:160780000-160781200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:160780200-160781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:160780200-160782000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:160780400-160781000	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr1:160780400-160781000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:160780400-160781000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:160780400-160781800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr1:160780400-160782200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:160780600-160781200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr1:160780600-160782000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:160780800-160781000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:160780800-160781000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:160780800-160781000	Enhancers	Esophagus	oesophagus
39	chr1:160780800-160781000	Enhancers	HMEC	breast
40	chr1:160780800-160781200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:160780800-160781200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:160780800-160781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:160780800-160782000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:160780800-160782800	Weak transcription	NHEK	skin
45	chr1:160780800-160787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links