Variant report

Variant	rs9838238
Chromosome Location	chr3:98600385-98600386
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	chr3:98595066..98597311-chr3:98599043..98600864,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12330381	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13317610	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13320266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327449	0.83[AMR][1000 genomes]
rs13327485	0.83[AMR][1000 genomes]
rs28417568	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28429424	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28528154	0.83[AMR][1000 genomes]
rs28650813	0.83[AMR][1000 genomes]
rs28821579	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28883308	0.83[AMR][1000 genomes]
rs28890260	0.83[AMR][1000 genomes]
rs3796133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56172805	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857413	0.94[ASN][1000 genomes]
rs57962467	0.94[ASN][1000 genomes]
rs59906228	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932691	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.83[ASN][1000 genomes]
rs72934623	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72934641	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72938577	0.94[ASN][1000 genomes]
rs9289699	0.83[AMR][1000 genomes]
rs9289700	0.83[AMR][1000 genomes]
rs9810407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819309	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9828045	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9833945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9842555	0.83[AMR][1000 genomes]
rs9848335	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9848583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852537	1.00[AMR][1000 genomes]
rs9862660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870500	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.83[AMR][1000 genomes]
rs9872301	0.83[AMR][1000 genomes]
rs9879302	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9883751	0.88[EUR][1000 genomes];1.00[ASN][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98578000-98601000	Weak transcription	Lung	lung
6	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:98584600-98604200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:98587200-98604600	Weak transcription	Ovary	ovary
10	chr3:98587800-98601800	Strong transcription	HSMM	muscle
11	chr3:98589200-98602200	Weak transcription	NHLF	lung
12	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
13	chr3:98589800-98604000	Weak transcription	Fetal Stomach	stomach
14	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:98590800-98604600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:98591400-98602200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:98591400-98604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:98591600-98604600	Weak transcription	Aorta	Aorta
19	chr3:98592600-98604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:98593800-98604600	Weak transcription	Psoas Muscle	Psoas
21	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
22	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
23	chr3:98594600-98600600	Strong transcription	HUVEC	blood vessel
24	chr3:98594600-98602200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr3:98594600-98604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:98595000-98603600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:98595200-98608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:98595600-98600400	Genic enhancers	NHEK	skin
29	chr3:98595600-98601800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:98596000-98604000	Weak transcription	K562	blood
31	chr3:98596200-98600800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:98596200-98601000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:98596200-98606600	Weak transcription	HepG2	liver
34	chr3:98596600-98600600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:98596800-98604200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:98597000-98600400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:98597000-98600400	Strong transcription	Fetal Lung	lung
38	chr3:98597000-98609000	Weak transcription	Right Ventricle	heart
39	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:98597600-98602400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:98597600-98602800	Strong transcription	HMEC	breast
42	chr3:98597800-98602800	Strong transcription	Osteobl	bone
43	chr3:98597800-98604200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:98598000-98600600	Weak transcription	Placenta	Placenta
45	chr3:98598000-98603800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:98598200-98602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:98598200-98608400	Weak transcription	Fetal Intestine Small	intestine
48	chr3:98598400-98601000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:98598400-98601600	Strong transcription	NHDF-Ad	bronchial
50	chr3:98598400-98604200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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