Variant report

Variant	rs1671687
Chromosome Location	chr12:123258583-123258584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11059729	1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12311043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1260121	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815479	1.00[CHD][hapmap]
rs1671684	1.00[JPT][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs3852535	0.81[EUR][1000 genomes]
rs4038080	0.81[EUR][1000 genomes]
rs4038081	0.81[EUR][1000 genomes]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs548349	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489241	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs839354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	1.00[ASN][1000 genomes]
rs839362	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1671687	TMEM120B	cis	parietal	SCAN
rs1671687	EIF2B1	cis	parietal	SCAN
rs1671687	RAB35	cis	parietal	SCAN
rs1671687	KDM2B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123238600-123258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123239600-123258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:123242000-123258600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:123242400-123258600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:123243800-123258600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123244800-123258800	Strong transcription	Dnd41	blood
7	chr12:123247800-123258600	Weak transcription	Right Atrium	heart
8	chr12:123251200-123258600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:123251200-123259600	Weak transcription	Fetal Heart	heart
10	chr12:123251400-123258600	Weak transcription	Pancreas	Pancrea
11	chr12:123251600-123258600	Weak transcription	Lung	lung
12	chr12:123251600-123258800	Weak transcription	Esophagus	oesophagus
13	chr12:123252000-123258600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:123252600-123258600	Weak transcription	Fetal Brain Male	brain
15	chr12:123252600-123258600	Weak transcription	Fetal Kidney	kidney
16	chr12:123252600-123258800	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:123252800-123258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:123252800-123258600	Weak transcription	Psoas Muscle	Psoas
19	chr12:123252800-123258800	Weak transcription	Small Intestine	intestine
20	chr12:123253000-123258600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:123253000-123258600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:123253000-123258600	Weak transcription	Brain Angular Gyrus	brain
23	chr12:123253000-123258600	Weak transcription	Brain Substantia Nigra	brain
24	chr12:123253000-123258800	Weak transcription	Aorta	Aorta
25	chr12:123253000-123258800	Weak transcription	Gastric	stomach
26	chr12:123253000-123258800	Weak transcription	Ovary	ovary
27	chr12:123253000-123258800	Weak transcription	Right Ventricle	heart
28	chr12:123253000-123258800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:123253000-123258800	Weak transcription	Spleen	Spleen
30	chr12:123253200-123258600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:123253400-123258600	Weak transcription	Brain Germinal Matrix	brain
32	chr12:123253600-123258600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:123253600-123258600	Weak transcription	Fetal Lung	lung
34	chr12:123253600-123258600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:123253600-123258600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:123253600-123258800	Weak transcription	HepG2	liver
37	chr12:123253600-123259200	Weak transcription	Hela-S3	cervix
38	chr12:123253600-123265200	Weak transcription	K562	blood
39	chr12:123254000-123258600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:123254400-123258600	Weak transcription	Colonic Mucosa	Colon
41	chr12:123254600-123258800	Weak transcription	Left Ventricle	heart
42	chr12:123255200-123258600	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:123255200-123258600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:123255600-123258600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:123255600-123258600	Weak transcription	Fetal Intestine Large	intestine
46	chr12:123255600-123258600	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:123255600-123258600	Weak transcription	HUVEC	blood vessel
48	chr12:123255600-123258800	Weak transcription	HSMMtube	muscle
49	chr12:123255800-123258600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:123255800-123258600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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