Variant report

Variant	rs17700142
Chromosome Location	chr7:38763391-38763392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1017028	0.85[ASN][1000 genomes]
rs10242048	0.85[ASN][1000 genomes]
rs10247503	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10251912	0.88[ASN][1000 genomes]
rs10254567	0.88[ASN][1000 genomes]
rs10271176	0.88[ASN][1000 genomes]
rs10486677	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10486678	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs11971020	0.90[ASN][1000 genomes]
rs11979618	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979824	0.90[ASN][1000 genomes]
rs11980882	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs12533557	0.88[ASN][1000 genomes]
rs12667567	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12672237	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12672750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672885	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs12674115	0.81[JPT][hapmap]
rs12701652	0.85[JPT][hapmap]
rs12701659	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1468348	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17700072	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17700172	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17700190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700262	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17700392	0.90[ASN][1000 genomes]
rs17700752	0.82[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.91[YRI][hapmap]
rs17767695	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17767770	0.99[ASN][1000 genomes]
rs17767818	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768153	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs17768212	0.90[ASN][1000 genomes]
rs17768711	0.82[CHB][hapmap]
rs17768753	0.85[JPT][hapmap]
rs1859494	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1859937	0.81[JPT][hapmap]
rs1978171	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1978172	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2074655	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs2074657	0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs2107743	0.88[ASN][1000 genomes]
rs2108507	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2189855	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2214666	0.90[ASN][1000 genomes]
rs2240351	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2240352	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2240353	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs2240354	0.88[ASN][1000 genomes]
rs2286082	0.87[ASN][1000 genomes]
rs2286084	0.90[ASN][1000 genomes]
rs2286086	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2286087	0.90[ASN][1000 genomes]
rs2286088	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs2286091	0.90[ASN][1000 genomes]
rs2286094	0.89[ASN][1000 genomes]
rs2286098	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs2286104	0.90[ASN][1000 genomes]
rs2286105	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2286106	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286109	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392598	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28548028	0.88[ASN][1000 genomes]
rs34724372	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs35253728	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35791079	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3735347	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs3801139	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801140	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801141	0.90[ASN][1000 genomes]
rs3801143	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801145	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3801146	0.88[ASN][1000 genomes]
rs4723782	0.88[ASN][1000 genomes]
rs4723785	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs56050717	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57091471	0.90[ASN][1000 genomes]
rs60590111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62444078	0.88[ASN][1000 genomes]
rs62444107	0.90[ASN][1000 genomes]
rs6462860	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66662538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66796288	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs66976998	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67202646	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733150	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs73368205	0.88[ASN][1000 genomes]
rs7778570	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7779329	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7780625	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs7783546	0.97[ASN][1000 genomes]
rs7783695	0.81[JPT][hapmap]
rs7785911	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7786389	0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs7794030	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7795874	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7797871	0.98[ASN][1000 genomes]
rs886646	0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]

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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17700142	C7orf10	cis	cerebellum	SCAN
rs17700142	EEPD1	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38756200-38763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:38756400-38764600	Weak transcription	Fetal Brain Female	brain
6	chr7:38756800-38764800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:38757000-38784200	Weak transcription	HMEC	breast
8	chr7:38757200-38764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:38757200-38764600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:38757200-38764600	Weak transcription	Ovary	ovary
11	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
12	chr7:38757400-38764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:38758600-38764400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:38758600-38764800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:38758600-38767000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:38758600-38767800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:38758800-38764400	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:38758800-38764400	Weak transcription	Lung	lung
20	chr7:38758800-38764800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:38758800-38765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:38758800-38766400	Weak transcription	Brain Germinal Matrix	brain
23	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
24	chr7:38759000-38764600	Weak transcription	NHLF	lung
25	chr7:38759000-38770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr7:38759200-38764800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:38759200-38810200	Weak transcription	A549	lung
28	chr7:38759400-38764600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:38759400-38764600	Weak transcription	Right Ventricle	heart
30	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:38759600-38764200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:38759600-38764200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:38759600-38764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:38759600-38764800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
36	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:38759800-38763400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:38759800-38764000	Weak transcription	HSMMtube	muscle
39	chr7:38759800-38764200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:38759800-38764600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr7:38759800-38764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:38759800-38765000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:38759800-38765000	Weak transcription	Fetal Lung	lung
44	chr7:38759800-38768000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:38760000-38764600	Weak transcription	Colonic Mucosa	Colon
47	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
49	chr7:38760400-38765200	Weak transcription	Colon Smooth Muscle	Colon
50	chr7:38760600-38764400	Weak transcription	Osteobl	bone

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