Variant report

Variant	rs12674115
Chromosome Location	chr7:38900191-38900192
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10247503	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10486677	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10486678	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs11980882	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12670221	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12672793	0.81[JPT][hapmap]
rs12672885	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs17700142	0.81[JPT][hapmap]
rs17700262	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17700752	0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs17767818	0.81[JPT][hapmap]
rs17768153	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs17768711	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17768753	0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1859937	0.81[JPT][hapmap]
rs2074655	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2074657	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs2108507	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2189855	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2240351	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2240352	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2240353	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2286086	0.80[CHB][hapmap]
rs2286088	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2286098	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2286105	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2286106	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2286109	0.81[JPT][hapmap]
rs2893567	0.82[JPT][hapmap]
rs34724372	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801129	0.83[ASN][1000 genomes]
rs3801139	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs3801140	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs3801143	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3801145	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4723785	0.82[CHB][hapmap]
rs61363591	0.98[ASN][1000 genomes]
rs6462872	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6956146	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6975048	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs733150	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs73357792	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7780490	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7780625	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs7785911	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7795874	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7800167	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs886646	0.83[JPT][hapmap]

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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12674115	STARD3NL	cis	lymphoblastoid	seeQTL
rs12674115	SEPT7	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
6	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
7	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
8	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
12	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:38877200-38900800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
16	chr7:38880600-38900600	Weak transcription	Adipose Nuclei	Adipose
17	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
18	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
20	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
21	chr7:38884600-38905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:38885000-38900800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:38886200-38901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:38886600-38901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:38886600-38907200	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:38887200-38906600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:38887200-38907400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:38887600-38902800	Weak transcription	Liver	Liver
33	chr7:38889200-38903000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:38889200-38907200	Weak transcription	Ovary	ovary
35	chr7:38889400-38900800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:38889400-38900800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:38889400-38906800	Weak transcription	Fetal Stomach	stomach
38	chr7:38889400-38907200	Weak transcription	Lung	lung
39	chr7:38889400-38907400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:38889400-38909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:38889400-38948200	Weak transcription	Gastric	stomach
42	chr7:38889600-38900800	Weak transcription	Dnd41	blood
43	chr7:38889600-38902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:38889600-38902400	Weak transcription	Fetal Intestine Small	intestine
45	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:38890000-38900800	Weak transcription	Primary T cells from cord blood	blood
47	chr7:38890800-38901000	Weak transcription	Placenta	Placenta
48	chr7:38891200-38903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
50	chr7:38894000-38903600	Weak transcription	Small Intestine	intestine

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