Variant report

Variant	rs759400
Chromosome Location	chr2:10709816-10709817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10167129	0.85[YRI][hapmap]
rs10181806	0.85[YRI][hapmap]
rs10191883	0.85[YRI][hapmap]
rs10195255	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195802	0.85[YRI][hapmap]
rs10201077	0.85[YRI][hapmap]
rs10203664	0.85[YRI][hapmap]
rs10203785	0.89[YRI][hapmap]
rs10210859	0.85[YRI][hapmap]
rs10454738	0.85[YRI][hapmap]
rs10929686	0.85[YRI][hapmap]
rs10929688	0.85[YRI][hapmap]
rs11683335	0.85[YRI][hapmap]
rs12464908	0.90[YRI][hapmap]
rs12692415	0.85[YRI][hapmap]
rs12692416	0.85[YRI][hapmap]
rs12692417	0.90[YRI][hapmap]
rs12692418	0.85[YRI][hapmap]
rs12995159	0.85[YRI][hapmap]
rs12995602	0.84[YRI][hapmap]
rs13034061	0.85[YRI][hapmap]
rs1309	0.86[LWK][hapmap]
rs17364568	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1990612	0.85[YRI][hapmap]
rs2010080	0.85[YRI][hapmap]
rs2110776	0.85[YRI][hapmap]
rs2110778	0.85[YRI][hapmap]
rs2287061	0.85[LWK][hapmap]
rs2287062	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs2357656	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs2884233	0.85[YRI][hapmap]
rs3814388	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs3815521	0.85[YRI][hapmap]
rs4233882	0.85[YRI][hapmap]
rs4233883	0.85[YRI][hapmap]
rs4331474	0.85[YRI][hapmap]
rs4453662	0.85[YRI][hapmap]
rs4470306	0.85[YRI][hapmap]
rs4519489	0.85[YRI][hapmap]
rs4555318	0.85[YRI][hapmap]
rs4613248	0.85[YRI][hapmap]
rs4614910	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs4668691	0.85[YRI][hapmap]
rs4669593	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs4669598	0.87[YRI][hapmap]
rs4669599	0.85[YRI][hapmap]
rs4669605	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4669606	0.83[CHD][hapmap];0.85[MEX][hapmap]
rs6432109	0.85[YRI][hapmap]
rs6432110	0.85[YRI][hapmap]
rs6432111	0.85[YRI][hapmap]
rs6432112	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs6432113	0.81[LWK][hapmap];0.85[YRI][hapmap]
rs6432114	0.85[YRI][hapmap]
rs6432115	0.81[YRI][hapmap]
rs6432116	0.85[YRI][hapmap]
rs6432117	0.85[YRI][hapmap]
rs6432119	0.89[YRI][hapmap]
rs6432120	0.85[YRI][hapmap]
rs6432122	0.85[YRI][hapmap]
rs6432126	0.81[YRI][hapmap]
rs6706542	0.85[YRI][hapmap]
rs6709466	0.85[YRI][hapmap]
rs6710033	0.82[YRI][hapmap]
rs6712406	0.85[YRI][hapmap]
rs6714413	0.85[YRI][hapmap]
rs6719701	0.90[YRI][hapmap]
rs6721510	0.85[YRI][hapmap]
rs6721514	0.85[YRI][hapmap]
rs6721739	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs6727884	0.85[YRI][hapmap]
rs6733416	0.85[YRI][hapmap]
rs6735074	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs6744599	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs6744854	0.85[YRI][hapmap]
rs6750891	0.85[YRI][hapmap]
rs6751075	0.85[YRI][hapmap]
rs6751398	0.85[YRI][hapmap]
rs6755548	0.85[YRI][hapmap]
rs6759714	0.85[YRI][hapmap]
rs6761678	0.85[YRI][hapmap]
rs715246	0.85[YRI][hapmap]
rs715247	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs728135	0.85[YRI][hapmap]
rs728281	0.85[YRI][hapmap]
rs728282	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs728283	0.89[YRI][hapmap]
rs7355649	0.85[YRI][hapmap]
rs7563816	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs7563894	0.85[YRI][hapmap]
rs7566767	0.85[YRI][hapmap]
rs7566875	0.85[YRI][hapmap]
rs7572631	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs7582775	0.85[YRI][hapmap]
rs7587114	0.85[YRI][hapmap]
rs7587231	0.85[YRI][hapmap]
rs7592691	0.85[YRI][hapmap]
rs7593496	0.85[YRI][hapmap]
rs759398	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs759403	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs7600495	0.85[YRI][hapmap]
rs7600587	0.85[YRI][hapmap]
rs7600695	0.85[YRI][hapmap]
rs7600728	0.85[YRI][hapmap]
rs7600820	0.85[YRI][hapmap]
rs7601748	0.85[YRI][hapmap]
rs7605461	0.85[YRI][hapmap]
rs7608498	0.85[YRI][hapmap]
rs9287720	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv833370	chr2:10625149-10785402	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1009897	chr2:10627248-10751468	Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs759400	NOL10	cis	parietal	SCAN
rs759400	CYS1	cis	cerebellum	SCAN
rs759400	OXSM	trans	parietal	SCAN
rs759400	C2orf50	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10689200-10710600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:10694200-10710000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:10696000-10710200	Weak transcription	Left Ventricle	heart
4	chr2:10696600-10710000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:10698600-10736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:10698800-10710400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:10699400-10711000	Weak transcription	GM12878-XiMat	blood
8	chr2:10699400-10716200	Weak transcription	Fetal Brain Male	brain
9	chr2:10700800-10710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:10700800-10710400	Weak transcription	Fetal Brain Female	brain
11	chr2:10701400-10710200	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:10701800-10710000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:10702000-10710200	Weak transcription	Ovary	ovary
14	chr2:10702000-10710200	Weak transcription	Right Atrium	heart
15	chr2:10702000-10715800	Weak transcription	Hela-S3	cervix
16	chr2:10702000-10717400	Weak transcription	Psoas Muscle	Psoas
17	chr2:10702200-10710400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:10702200-10713800	Weak transcription	K562	blood
19	chr2:10703400-10710200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:10705000-10711800	Weak transcription	Osteobl	bone
21	chr2:10705000-10712400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:10705200-10711000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:10705400-10711200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:10705600-10711200	Weak transcription	Fetal Lung	lung
25	chr2:10705800-10736000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:10706000-10713800	Weak transcription	HSMMtube	muscle
27	chr2:10706400-10710000	Weak transcription	Brain Angular Gyrus	brain
28	chr2:10706400-10710000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:10706400-10710200	Weak transcription	A549	lung
30	chr2:10706400-10710200	Weak transcription	HMEC	breast
31	chr2:10706400-10713800	Weak transcription	Brain Substantia Nigra	brain
32	chr2:10706400-10716000	Weak transcription	Fetal Kidney	kidney
33	chr2:10706400-10716600	Strong transcription	Fetal Intestine Small	intestine
34	chr2:10707000-10710400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:10707200-10711600	Weak transcription	HUVEC	blood vessel
36	chr2:10707400-10710200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:10707400-10711200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:10707400-10728800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:10708000-10710200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:10708400-10713000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:10708600-10710000	Strong transcription	Brain Hippocampus Middle	brain
42	chr2:10708600-10710400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:10708600-10710400	Enhancers	NHDF-Ad	bronchial
44	chr2:10708600-10710600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:10708600-10710600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr2:10708600-10711200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:10708600-10712200	Strong transcription	Gastric	stomach
48	chr2:10708600-10718600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:10708600-10718800	Strong transcription	Primary T cells from cord blood	blood
50	chr2:10708600-10719600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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