Variant report

Variant	rs9862660
Chromosome Location	chr3:98512417-98512418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes]
rs13317610	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	0.88[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28417568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429424	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs3796133	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]
rs56172805	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56857413	0.82[ASN][1000 genomes]
rs57962467	0.82[ASN][1000 genomes]
rs59906228	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72932691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934623	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938577	0.82[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.88[ASN][1000 genomes]
rs9812438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9833945	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9836915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9838166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9838238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes]
rs9848583	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[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes]
rs9883751	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
12	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
13	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
14	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:98499800-98514800	Weak transcription	Dnd41	blood
18	chr3:98501200-98513400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
20	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:98502600-98513400	Weak transcription	Fetal Stomach	stomach
23	chr3:98503200-98513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:98503400-98518200	Weak transcription	Ovary	ovary
25	chr3:98503400-98576400	Weak transcription	Gastric	stomach
26	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:98504600-98517000	Weak transcription	HSMMtube	muscle
28	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
30	chr3:98504800-98514000	Weak transcription	NHEK	skin
31	chr3:98504800-98515000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:98504800-98517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:98505000-98515200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:98505400-98513400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:98505400-98513400	Weak transcription	Lung	lung
37	chr3:98505400-98515200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:98505400-98518400	Weak transcription	Fetal Thymus	thymus
39	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
40	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
41	chr3:98505600-98512600	Weak transcription	NHDF-Ad	bronchial
42	chr3:98505600-98512800	Weak transcription	HSMM	muscle
43	chr3:98505800-98513400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:98505800-98513600	Weak transcription	Adipose Nuclei	Adipose
45	chr3:98505800-98514200	Weak transcription	NHLF	lung
46	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
47	chr3:98506000-98513800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:98506000-98514000	Weak transcription	HMEC	breast
49	chr3:98506000-98515200	Weak transcription	Aorta	Aorta
50	chr3:98506200-98513400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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