Variant report

Variant	rs3935544
Chromosome Location	chr9:94532795-94532796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94530728..94533133-chr9:94548212..94550355,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10512217	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs10820902	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10820903	0.81[AMR][1000 genomes]
rs10992086	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs10992090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992104	0.83[AMR][1000 genomes]
rs10992108	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10992109	0.83[AMR][1000 genomes]
rs12235606	0.86[AFR][1000 genomes]
rs12235611	0.86[AFR][1000 genomes]
rs12237459	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs12237573	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12238428	0.84[YRI][hapmap]
rs12685213	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12685849	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs16907741	0.86[AFR][1000 genomes]
rs16907754	0.83[AFR][1000 genomes]
rs16907768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178196	0.83[AMR][1000 genomes]
rs2312730	0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3802377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322069	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4398991	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4400454	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4452868	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4595186	0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs4601388	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57810120	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58210546	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58462029	0.97[EUR][1000 genomes]
rs60092492	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs60617711	0.97[EUR][1000 genomes]
rs73511086	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73513203	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73513246	0.98[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73651508	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv6612	chr9:94490644-94535738	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
2	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:94521200-94532800	Weak transcription	Ovary	ovary
4	chr9:94524400-94533000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:94527000-94533000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94527200-94533200	Weak transcription	Fetal Intestine Large	intestine
7	chr9:94527600-94538800	Weak transcription	K562	blood
8	chr9:94528600-94533200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:94529200-94532800	Weak transcription	Fetal Lung	lung
10	chr9:94529400-94539800	Enhancers	Colon Smooth Muscle	Colon
11	chr9:94530400-94535200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:94531400-94533000	Genic enhancers	Fetal Stomach	stomach
13	chr9:94531600-94533000	Weak transcription	Fetal Intestine Small	intestine
14	chr9:94531600-94533600	Enhancers	Esophagus	oesophagus
15	chr9:94532200-94533200	Enhancers	Rectal Smooth Muscle	rectum
16	chr9:94532200-94537000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr9:94532200-94539200	Enhancers	Fetal Heart	heart
18	chr9:94532400-94532800	Enhancers	NHEK	skin
19	chr9:94532400-94533000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:94532400-94533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:94532400-94533000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr9:94532400-94533400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:94532400-94533600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr9:94532400-94534600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:94532600-94532800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:94532600-94532800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:94532600-94532800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:94532600-94533000	Enhancers	Right Atrium	heart
29	chr9:94532600-94533200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:94532600-94533200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:94532600-94533200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:94532600-94533200	Enhancers	Duodenum Mucosa	Duodenum
33	chr9:94532600-94533400	Enhancers	Fetal Brain Male	brain
34	chr9:94532600-94533400	Enhancers	Fetal Thymus	thymus
35	chr9:94532600-94533600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:94532600-94533600	Enhancers	Placenta	Placenta
37	chr9:94532600-94534000	Enhancers	HMEC	breast
38	chr9:94532600-94534400	Enhancers	Placenta Amnion	Placenta Amnion

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