Variant report

Variant	rs2352969
Chromosome Location	chr3:50003632-50003633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1061474	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs1062633	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10865959	0.86[CHB][hapmap]
rs11130222	0.85[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs1138536	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs11709573	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11712056	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11714324	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11721204	0.95[ASN][1000 genomes]
rs12107768	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12496973	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13060128	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.98[ASN][1000 genomes]
rs13079006	0.95[ASN][1000 genomes]
rs13082703	0.95[ASN][1000 genomes]
rs1317140	0.89[CHB][hapmap]
rs17657664	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17657688	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1799843	0.89[CHB][hapmap]
rs1799845	0.89[CHB][hapmap]
rs2013208	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2230590	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240326	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240327	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240328	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs2240329	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2247510	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2252833	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2276864	0.86[CHB][hapmap]
rs2280406	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2352975	0.89[CHB][hapmap]
rs2352984	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2526748	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526751	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526754	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624815	0.82[ASN][1000 genomes]
rs2624817	0.80[ASN][1000 genomes]
rs2624819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2624821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2624826	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs2624832	0.95[ASN][1000 genomes]
rs2624834	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs2624843	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624847	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2624853	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.95[ASN][1000 genomes]
rs2681779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681780	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681781	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2777888	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2856234	0.85[CHD][hapmap]
rs2856237	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2856238	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs2883057	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2883059	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34034116	0.95[ASN][1000 genomes]
rs34312088	0.95[ASN][1000 genomes]
rs34654589	0.87[ASN][1000 genomes]
rs35275715	0.95[ASN][1000 genomes]
rs36022378	0.85[ASN][1000 genomes]
rs3733134	0.95[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3774759	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3796386	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4688688	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688689	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4688754	0.82[ASN][1000 genomes]
rs4688755	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs55692411	0.87[ASN][1000 genomes]
rs62262114	0.95[ASN][1000 genomes]
rs6446193	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6446195	0.82[ASN][1000 genomes]
rs6762477	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6765484	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6792892	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6799579	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7061	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7430334	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7613360	0.84[ASN][1000 genomes]
rs7613875	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7621026	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.92[ASN][1000 genomes]
rs7627864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7627910	0.92[ASN][1000 genomes]
rs7628058	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7629936	0.89[CHB][hapmap]
rs7634441	0.82[ASN][1000 genomes]
rs7648174	0.95[ASN][1000 genomes]
rs868891	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9311446	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs952594	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9682295	0.82[ASN][1000 genomes]
rs9814664	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9861216	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9866695	0.85[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2352969	NCKIPSD	cis	parietal	SCAN
rs2352969	RBM6	cis	multi-tissue	Pritchard
rs2352969	CYB561D2	cis	cerebellum	SCAN
rs2352969	C3orf78	cis	parietal	SCAN
rs2352969	RBM6	cis	parietal	SCAN
rs2352969	RBM6	cis	cerebellum	SCAN
rs2352969	NCKIPSD	cis	cerebellum	SCAN
rs2352969	C3orf18	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
4	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:49979000-50005200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:49979000-50010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:49979600-50004200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:49988000-50004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:49988200-50007000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:49988200-50007400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:49988200-50010200	Weak transcription	Gastric	stomach
12	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:49988400-50009600	Weak transcription	Fetal Brain Female	brain
14	chr3:49988400-50009600	Weak transcription	HUVEC	blood vessel
15	chr3:49988800-50004800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:49989000-50004000	Weak transcription	Pancreas	Pancrea
17	chr3:49991200-50005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:49995000-50005200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
21	chr3:49995600-50005800	Weak transcription	Spleen	Spleen
22	chr3:49996600-50010200	Weak transcription	Lung	lung
23	chr3:49997000-50010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:49997600-50007400	Weak transcription	Right Atrium	heart
25	chr3:49997600-50009600	Weak transcription	A549	lung
26	chr3:49997800-50004000	Weak transcription	Brain Anterior Caudate	brain
27	chr3:49997800-50004000	Weak transcription	Left Ventricle	heart
28	chr3:49997800-50009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:49997800-50009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:49997800-50013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49998200-50003800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:49998200-50003800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:49998200-50007600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:49998400-50003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:49998400-50003800	Weak transcription	NHLF	lung
37	chr3:49998400-50004000	Weak transcription	NHDF-Ad	bronchial
38	chr3:49998400-50004800	Weak transcription	Thymus	Thymus
39	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
40	chr3:49998400-50078600	Weak transcription	K562	blood
41	chr3:49998800-50003800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:49998800-50004200	Weak transcription	Psoas Muscle	Psoas
43	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:49999000-50004000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:49999000-50007800	Strong transcription	Fetal Thymus	thymus
46	chr3:49999600-50004000	Weak transcription	Ovary	ovary
47	chr3:49999600-50006800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:49999600-50007800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:49999800-50006200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:49999800-50011000	Strong transcription	Monocytes-CD14+_RO01746	blood

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