Variant report

Variant	rs1678169
Chromosome Location	chr2:231338211-231338212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1051579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1051580	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1051581	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1278	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1382699	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1479177	0.96[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1564322	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1564323	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1600297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1613630	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649863	0.86[ASW][hapmap];0.81[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1649864	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649866	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649867	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649875	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1649878	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1649882	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649886	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649887	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649888	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649889	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649928	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678163	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678164	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678165	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678167	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678200	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678201	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678202	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678203	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678204	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17274304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17333468	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333482	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333503	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303609	1.00[CEU][hapmap]
rs2306274	1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[ASN][1000 genomes]
rs2306276	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2434048	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2559088	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619159	0.83[ASN][1000 genomes]
rs3769853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769856	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6436938	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739283	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73000277	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7878	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1678169	SP100	Cis_1M	lymphoblastoid	RTeQTL
rs1678169	UGT1A1	cis	cerebellum	SCAN
rs1678169	NMUR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
2	chr2:231301800-231345000	Weak transcription	A549	lung
3	chr2:231321800-231338600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:231322200-231340200	Strong transcription	Liver	Liver
5	chr2:231325800-231338400	Strong transcription	Left Ventricle	heart
6	chr2:231325800-231338600	Strong transcription	Lung	lung
7	chr2:231325800-231338800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:231328200-231338400	Strong transcription	Fetal Muscle Leg	muscle
9	chr2:231329600-231343800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:231331200-231338400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:231332000-231345200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:231332400-231344400	Weak transcription	Gastric	stomach
13	chr2:231332800-231339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:231333400-231339800	Genic enhancers	Primary B cells from cord blood	blood
15	chr2:231334200-231356000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:231334600-231340000	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr2:231334800-231358400	Weak transcription	Fetal Stomach	stomach
18	chr2:231335000-231344400	Weak transcription	Aorta	Aorta
19	chr2:231335000-231359000	Weak transcription	NHLF	lung
20	chr2:231335600-231339000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:231335600-231340200	Weak transcription	Fetal Intestine Large	intestine
22	chr2:231335600-231344600	Weak transcription	Pancreas	Pancrea
23	chr2:231336000-231343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:231336000-231344400	Weak transcription	Esophagus	oesophagus
25	chr2:231336000-231356000	Weak transcription	NHDF-Ad	bronchial
26	chr2:231336200-231342200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:231336200-231344400	Weak transcription	HSMMtube	muscle
28	chr2:231336400-231338400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:231336400-231339200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:231336400-231339400	Weak transcription	Psoas Muscle	Psoas
31	chr2:231336400-231343800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:231336400-231345200	Weak transcription	Small Intestine	intestine
33	chr2:231336400-231363400	Weak transcription	Fetal Lung	lung
34	chr2:231336600-231338400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:231336600-231339000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:231336600-231340000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:231336600-231342200	Weak transcription	Ovary	ovary
38	chr2:231336600-231344200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:231336600-231345000	Weak transcription	Spleen	Spleen
40	chr2:231336600-231356200	Weak transcription	Placenta	Placenta
41	chr2:231336600-231363400	Weak transcription	Right Ventricle	heart
42	chr2:231336800-231339200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:231336800-231339400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:231336800-231339400	Weak transcription	Adipose Nuclei	Adipose
45	chr2:231336800-231339400	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:231336800-231343400	Weak transcription	HSMM	muscle
47	chr2:231336800-231343800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:231336800-231344200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:231336800-231376000	Weak transcription	Colonic Mucosa	Colon
50	chr2:231337000-231338800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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