Variant report

Variant	rs9634680
Chromosome Location	chr13:49161082-49161083
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11148110	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12855185	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12859099	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12876717	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12877288	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12877954	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359688	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536396	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1536397	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808060	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1887154	0.80[EUR][1000 genomes]
rs1894255	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap]
rs1951775	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs198584	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs198590	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs198604	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]
rs198607	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs198612	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2104532	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406935	0.83[EUR][1000 genomes]
rs2407093	0.88[EUR][1000 genomes]
rs2407095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897588	0.81[EUR][1000 genomes]
rs3092904	0.85[EUR][1000 genomes]
rs4497565	0.80[EUR][1000 genomes]
rs4635233	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139578	0.86[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs7325719	0.82[EUR][1000 genomes]
rs7329065	0.86[EUR][1000 genomes]
rs7333360	0.84[EUR][1000 genomes]
rs7336379	0.88[EUR][1000 genomes]
rs8002098	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316381	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs9316388	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316393	0.87[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316394	0.83[EUR][1000 genomes]
rs9316395	0.86[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9316399	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs9316407	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9331991	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs943278	0.86[CEU][hapmap]
rs943280	0.92[EUR][1000 genomes]
rs943283	0.81[EUR][1000 genomes]
rs9526479	0.83[EUR][1000 genomes]
rs9526481	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526483	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535032	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs9535038	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535042	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535043	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535045	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535046	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535049	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9568047	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568049	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568050	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568051	0.82[EUR][1000 genomes]
rs990814	0.86[CEU][hapmap];0.83[TSI][hapmap]

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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9634680	LPAR6	cis	parietal	SCAN
rs9634680	C13orf1	cis	cerebellum	SCAN
rs9634680	ATAD2	trans	parietal	SCAN
rs9634680	ITM2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49156000-49161400	Enhancers	HepG2	liver
2	chr13:49156400-49161400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:49157400-49161200	Enhancers	HSMMtube	muscle
4	chr13:49157600-49164800	Weak transcription	Gastric	stomach
5	chr13:49157800-49161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:49158000-49161400	Enhancers	Colon Smooth Muscle	Colon
7	chr13:49158000-49161600	Enhancers	HMEC	breast
8	chr13:49158000-49161600	Enhancers	HUVEC	blood vessel
9	chr13:49158200-49161400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr13:49158400-49161200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr13:49158600-49161200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:49158600-49161200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:49158600-49161200	Enhancers	Brain Cingulate Gyrus	brain
14	chr13:49158600-49161200	Enhancers	Stomach Mucosa	stomach
15	chr13:49158600-49161400	Enhancers	Adipose Nuclei	Adipose
16	chr13:49158600-49161400	Enhancers	Fetal Muscle Leg	muscle
17	chr13:49158800-49161200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr13:49158800-49161400	Enhancers	Brain Angular Gyrus	brain
19	chr13:49158800-49161400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:49158800-49161400	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr13:49158800-49161400	Enhancers	Rectal Smooth Muscle	rectum
22	chr13:49158800-49161400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr13:49159000-49162200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:49159200-49161200	Enhancers	Fetal Lung	lung
25	chr13:49159200-49161400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:49159200-49161400	Enhancers	Brain Substantia Nigra	brain
27	chr13:49159200-49161400	Enhancers	Duodenum Mucosa	Duodenum
28	chr13:49159200-49163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:49159400-49161200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:49159400-49161200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr13:49159400-49161200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr13:49159400-49161600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr13:49159600-49161200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr13:49159600-49161200	Enhancers	Fetal Heart	heart
35	chr13:49159600-49161400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:49159600-49161600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr13:49159600-49161600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:49159600-49161800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr13:49159600-49162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:49159800-49161200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr13:49159800-49161400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr13:49159800-49164200	Weak transcription	Small Intestine	intestine
43	chr13:49160000-49166000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr13:49160200-49161400	Enhancers	Primary T cells from cord blood	blood
45	chr13:49160200-49161400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr13:49160200-49161600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr13:49160200-49166200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:49160400-49161400	Enhancers	Primary B cells from cord blood	blood
49	chr13:49160400-49161400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr13:49160400-49161400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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