Variant report

Variant	rs3768688
Chromosome Location	chr2:148671101-148671102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10180655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10439198	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11686483	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105745	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1227304	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234416	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12622150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12989087	0.94[ASN][1000 genomes]
rs13016400	0.82[CEU][hapmap]
rs13016893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13430086	0.89[CEU][hapmap];0.96[ASN][1000 genomes]
rs1895694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113792	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113794	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2194695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603597	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2603600	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2627019	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2627025	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3768684	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3768686	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3820716	0.89[CEU][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4419186	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55816333	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56073268	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709182	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6713811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731371	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7593570	0.91[ASN][1000 genomes]
rs9287411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3768688	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148642800-148674600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:148645800-148671400	Weak transcription	Fetal Heart	heart
4	chr2:148646200-148684400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:148646600-148671200	Weak transcription	HMEC	breast
6	chr2:148646600-148691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
8	chr2:148649600-148674800	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:148651200-148691600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:148652800-148690000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:148652800-148693600	Weak transcription	Lung	lung
13	chr2:148653200-148692000	Weak transcription	Ovary	ovary
14	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
15	chr2:148653600-148671400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:148653600-148673400	Weak transcription	HepG2	liver
17	chr2:148653800-148671600	Weak transcription	Fetal Stomach	stomach
18	chr2:148653800-148672800	Weak transcription	Liver	Liver
19	chr2:148654000-148690000	Weak transcription	Primary T cells from cord blood	blood
20	chr2:148655200-148674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:148655400-148671600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:148655800-148671200	Weak transcription	Fetal Brain Male	brain
23	chr2:148656200-148676800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:148657800-148674400	Weak transcription	Fetal Kidney	kidney
25	chr2:148657800-148674400	Weak transcription	Left Ventricle	heart
26	chr2:148657800-148683000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:148658000-148671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:148658000-148672600	Weak transcription	Fetal Intestine Large	intestine
29	chr2:148658600-148674400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
31	chr2:148659600-148719800	Weak transcription	Gastric	stomach
32	chr2:148660200-148673400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:148661200-148673400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:148661600-148718200	Weak transcription	Fetal Intestine Small	intestine
35	chr2:148662000-148683800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:148662400-148671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:148663000-148692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:148664000-148671200	Weak transcription	HSMM	muscle
39	chr2:148664200-148672800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:148664600-148721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:148664800-148693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:148668600-148671600	Weak transcription	Adipose Nuclei	Adipose
43	chr2:148668600-148674800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:148668600-148682400	Weak transcription	Psoas Muscle	Psoas
45	chr2:148668600-148683600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:148668600-148691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:148668800-148683400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:148669000-148671400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:148669000-148671400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:148669000-148671400	Weak transcription	Fetal Lung	lung

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