Variant report

Variant	rs12501247
Chromosome Location	chr4:48258877-48258878
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48255521..48259627-chr4:48261501..48267509,10	K562	blood:
2	chr4:48250701..48254731-chr4:48255352..48259390,5	K562	blood:
3	chr4:48256167..48259627-chr4:48260322..48264297,6	K562	blood:
4	chr4:48257479..48259057-chr4:48261577..48263259,2	MCF-7	breast:
5	chr4:48258706..48261232-chr4:48269979..48272552,2	MCF-7	breast:
6	chr4:48255045..48260439-chr4:48268334..48274456,6	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10938526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501146	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12508645	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13113745	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129386	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1472972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1472973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28410946	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695364	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676110	0.80[CEU][hapmap]
rs7681182	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681186	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7697203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291322	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2763359	chr4:48189710-48290233	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv461357	chr4:48248258-48274152	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv594119	chr4:48248258-48274152	Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv470032	chr4:48251915-48312389	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv461358	chr4:48251916-48274152	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv594120	chr4:48251916-48274152	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
11	nsv4329	chr4:48254113-48262973	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12501247	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48248800-48270600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:48249600-48261600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:48250600-48259400	Weak transcription	Small Intestine	intestine
4	chr4:48251400-48270000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:48251800-48270200	Weak transcription	Fetal Intestine Large	intestine
6	chr4:48253000-48263000	Weak transcription	Primary B cells from cord blood	blood
7	chr4:48256800-48264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:48257000-48263600	Weak transcription	HSMM	muscle
9	chr4:48257400-48270600	Weak transcription	Right Ventricle	heart
10	chr4:48257400-48271000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:48257400-48271200	Weak transcription	Esophagus	oesophagus
12	chr4:48257600-48265000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:48257600-48271200	Weak transcription	Gastric	stomach
14	chr4:48257800-48261400	Weak transcription	Liver	Liver
15	chr4:48257800-48261600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:48257800-48263000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:48258000-48259800	Enhancers	K562	blood
18	chr4:48258000-48263000	Weak transcription	Fetal Lung	lung
19	chr4:48258000-48270800	Weak transcription	Fetal Intestine Small	intestine
20	chr4:48258200-48259600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:48258200-48263000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:48258400-48259400	Weak transcription	Fetal Thymus	thymus
23	chr4:48258400-48259400	Weak transcription	GM12878-XiMat	blood
24	chr4:48258400-48269400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:48258400-48270000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:48258400-48271200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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