Variant report

Variant	rs2306042
Chromosome Location	chr9:93641151-93641152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93633763..93637108-chr9:93639159..93643075,3	MCF-7	breast:
2	chr9:93636708..93639399-chr9:93641106..93642988,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10993708	1.00[TSI][hapmap]
rs10993710	1.00[TSI][hapmap]
rs10993714	1.00[TSI][hapmap]
rs10993730	1.00[AMR][1000 genomes]
rs10993738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs10993740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12684347	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2991216	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs59057775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59844916	1.00[ASN][1000 genomes]
rs60516153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72729078	0.99[ASN][1000 genomes]
rs72729082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv430078	chr9:93609668-93642766	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv430079	chr9:93620963-93642766	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv416495	chr9:93638584-93643961	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv416141	chr9:93638589-93643961	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2306042	NFIL3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
3	chr9:93623600-93642400	Weak transcription	Adipose Nuclei	Adipose
4	chr9:93625000-93642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:93625200-93642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:93626000-93647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:93630000-93644800	Weak transcription	Pancreas	Pancrea
8	chr9:93632600-93641600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr9:93633400-93645800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:93633800-93645400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:93634000-93642600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:93634000-93645800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr9:93634000-93646200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:93634000-93646400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:93634000-93666200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:93634400-93646600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr9:93635600-93646200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr9:93636000-93644000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:93636400-93650600	Weak transcription	Liver	Liver
20	chr9:93637200-93642400	Weak transcription	Lung	lung
21	chr9:93637200-93642400	Weak transcription	Small Intestine	intestine
22	chr9:93638200-93641800	Strong transcription	Primary B cells from cord blood	blood
23	chr9:93638800-93646800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr9:93639400-93642800	Strong transcription	Spleen	Spleen
25	chr9:93639400-93643400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:93639400-93643600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:93639400-93643600	Strong transcription	Gastric	stomach
28	chr9:93639400-93645600	Strong transcription	Thymus	Thymus
29	chr9:93639400-93645800	Strong transcription	Fetal Thymus	thymus
30	chr9:93639400-93646200	Strong transcription	Fetal Stomach	stomach
31	chr9:93639400-93646400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:93639400-93647000	Weak transcription	HMEC	breast
33	chr9:93639800-93643400	Strong transcription	Fetal Intestine Large	intestine
34	chr9:93640000-93646400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr9:93640200-93641600	Weak transcription	Colonic Mucosa	Colon
36	chr9:93640200-93642400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:93640400-93642400	Strong transcription	GM12878-XiMat	blood
38	chr9:93640600-93641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:93640600-93641200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:93640600-93641400	Enhancers	NHEK	skin
41	chr9:93640600-93641800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:93640600-93641800	Strong transcription	K562	blood
43	chr9:93640800-93642400	Weak transcription	Fetal Intestine Small	intestine
44	chr9:93640800-93642600	Strong transcription	Fetal Kidney	kidney
45	chr9:93641000-93642400	Weak transcription	Esophagus	oesophagus

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