Variant report

Variant	rs4017732
Chromosome Location	chr1:160780555-160780556
allele	G/T
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	TEAD4	chr1:160780317-160780594	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr1:160780271-160780665	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr1:160780272-160780686	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:160779866..160781807-chr1:160913798..160915545,2	MCF-7	breast:
2	chr1:160776649..160779858-chr1:160780478..160783432,4	K562	blood:
3	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: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11265489	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2090755	0.84[ASN][1000 genomes]
rs35237586	0.87[ASN][1000 genomes]
rs532466	0.84[ASN][1000 genomes]
rs6667581	0.94[YRI][hapmap]
rs7555175	0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4017732	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs4017732	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 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	chr1:160777800-160780800	Weak transcription	Esophagus	oesophagus
9	chr1:160778000-160780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:160778000-160782800	Weak transcription	GM12878-XiMat	blood
11	chr1:160778000-160783000	Weak transcription	Fetal Thymus	thymus
12	chr1:160778000-160783000	Weak transcription	Thymus	Thymus
13	chr1:160778000-160783800	Weak transcription	Spleen	Spleen
14	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:160778400-160780800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:160778400-160783200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:160778600-160780600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:160778600-160783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:160779200-160780800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:160779600-160780600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:160779600-160781600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:160779800-160781000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:160779800-160781200	Enhancers	Placenta	Placenta
26	chr1:160779800-160789200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:160780000-160781000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:160780000-160781000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:160780000-160781200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:160780000-160781200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:160780000-160781200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:160780200-160781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:160780200-160782000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:160780400-160780800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:160780400-160780800	Enhancers	NHEK	skin
37	chr1:160780400-160781000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:160780400-160781000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:160780400-160781000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:160780400-160781800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:160780400-160782200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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