Variant report

Variant	rs940525
Chromosome Location	chr7:27560822-27560823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1005128	1.00[ASN][1000 genomes]
rs1009252	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1014373	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1015750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1030003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10447552	0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1052724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1052741	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10807841	1.00[ASN][1000 genomes]
rs10951169	1.00[ASN][1000 genomes]
rs10951171	1.00[ASN][1000 genomes]
rs10951172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951175	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10951176	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1111647	1.00[ASN][1000 genomes]
rs11526176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767188	1.00[ASN][1000 genomes]
rs12155430	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12164139	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12530626	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12535844	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12537499	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12540276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665991	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12667235	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12667610	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12668430	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12670415	0.93[ASN][1000 genomes]
rs12700813	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12700819	0.90[ASN][1000 genomes]
rs12700822	0.90[ASN][1000 genomes]
rs12700826	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13226102	0.83[ASN][1000 genomes]
rs13227873	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13237776	1.00[JPT][hapmap]
rs13242248	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13244903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13246464	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13308974	0.83[ASN][1000 genomes]
rs1357760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1404276	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1404278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1524526	0.90[ASN][1000 genomes]
rs1524530	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1524531	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1524532	1.00[ASN][1000 genomes]
rs1524533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1554641	1.00[ASN][1000 genomes]
rs1608664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17155546	1.00[JPT][hapmap]
rs1851911	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851912	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1880370	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1980329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1986243	1.00[ASN][1000 genomes]
rs2041714	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2080245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2080246	1.00[ASN][1000 genomes]
rs2091171	1.00[ASN][1000 genomes]
rs2098315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2098316	1.00[ASN][1000 genomes]
rs2110526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2110528	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2391443	1.00[ASN][1000 genomes]
rs2391452	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2391453	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28416309	0.96[ASN][1000 genomes]
rs28429439	1.00[ASN][1000 genomes]
rs34886410	1.00[ASN][1000 genomes]
rs3847001	1.00[ASN][1000 genomes]
rs3925338	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4140899	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs42085	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs42099	1.00[JPT][hapmap]
rs4348389	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4719898	1.00[ASN][1000 genomes]
rs4719899	0.82[ASN][1000 genomes]
rs4719900	1.00[ASN][1000 genomes]
rs4719902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4722719	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4722724	0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs4722728	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6415251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462026	1.00[ASN][1000 genomes]
rs6462029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6462031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6462032	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462036	0.93[ASN][1000 genomes]
rs6462037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6462038	1.00[JPT][hapmap]
rs6945993	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6946075	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6947731	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6948814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6949496	1.00[ASN][1000 genomes]
rs6955074	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6956484	1.00[ASN][1000 genomes]
rs6957674	1.00[ASN][1000 genomes]
rs6958747	0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6959126	0.85[ASN][1000 genomes]
rs6959495	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6960834	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6961429	1.00[JPT][hapmap]
rs6963421	1.00[JPT][hapmap]
rs6963585	1.00[ASN][1000 genomes]
rs6964190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966918	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970104	0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6974052	1.00[ASN][1000 genomes]
rs6974387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6974932	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6980382	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs723699	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs723700	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7455882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs759269	1.00[ASN][1000 genomes]
rs7778320	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7779240	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780431	1.00[ASN][1000 genomes]
rs7783447	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7794292	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7806605	1.00[ASN][1000 genomes]
rs7806812	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7811436	0.93[ASN][1000 genomes]
rs940526	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9639553	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9639560	1.00[ASN][1000 genomes]
rs978447	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs986706	1.00[CHB][hapmap];1.00[JPT][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	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs940525	SCRN1	cis	cerebellum	SCAN
rs940525	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27549200-27561200	Weak transcription	Liver	Liver
2	chr7:27550600-27563400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:27551200-27563800	Weak transcription	Left Ventricle	heart
4	chr7:27551600-27563800	Weak transcription	Placenta	Placenta
5	chr7:27552600-27564800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:27552600-27568200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:27553000-27563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:27553200-27581000	Weak transcription	Fetal Heart	heart
9	chr7:27553600-27564000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:27553800-27564600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:27554400-27564000	Weak transcription	K562	blood
12	chr7:27555000-27568600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:27555800-27581000	Weak transcription	Gastric	stomach
14	chr7:27556000-27562800	Weak transcription	Aorta	Aorta
15	chr7:27556000-27563800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:27556000-27579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:27556000-27581600	Weak transcription	HMEC	breast
18	chr7:27556200-27564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:27556400-27564400	Weak transcription	Brain Substantia Nigra	brain
20	chr7:27556400-27584400	Weak transcription	NHEK	skin
21	chr7:27556400-27586400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:27556600-27563800	Weak transcription	Fetal Kidney	kidney
23	chr7:27556600-27563800	Weak transcription	Dnd41	blood
24	chr7:27556600-27568400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr7:27556600-27569000	Weak transcription	NHDF-Ad	bronchial
26	chr7:27556800-27568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:27557000-27564200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:27557200-27573400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:27557600-27564200	Enhancers	Fetal Lung	lung
30	chr7:27558000-27561200	Enhancers	Colon Smooth Muscle	Colon
31	chr7:27558000-27561800	Enhancers	Fetal Stomach	stomach
32	chr7:27558000-27579800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:27558200-27563600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:27558200-27563600	Weak transcription	Ovary	ovary
35	chr7:27558200-27563800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:27558200-27563800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:27558200-27564600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:27558200-27566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:27558400-27561600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:27558400-27563800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:27558400-27563800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:27558400-27564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:27558400-27565200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:27558600-27563800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:27558600-27565200	Weak transcription	HepG2	liver
46	chr7:27558600-27566400	Weak transcription	Fetal Intestine Small	intestine
47	chr7:27558600-27568200	Weak transcription	Right Ventricle	heart
48	chr7:27558800-27563800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:27558800-27563800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:27559400-27561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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