Variant report

Variant	rs2088666
Chromosome Location	chr3:196010434-196010435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196009871..196011418-chr3:196018699..196020809,2	K562	blood:

Variant related genes	Relation type
ENSG00000213123	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11914521	0.81[ASN][1000 genomes]
rs11929532	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12629949	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630070	0.85[JPT][hapmap]
rs12632779	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs12633502	0.83[ASN][1000 genomes]
rs12634304	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634587	0.81[JPT][hapmap]
rs12637288	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs12637379	0.81[ASN][1000 genomes]
rs1357289	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs1948690	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047550	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap]
rs2047551	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270769	0.85[JPT][hapmap]
rs2293160	0.85[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3772109	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396926	1.00[ASN][1000 genomes]
rs4916421	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916424	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4916425	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4916456	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916477	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4916485	0.81[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs55878253	0.81[ASN][1000 genomes]
rs55996879	0.85[ASN][1000 genomes]
rs56240083	0.81[ASN][1000 genomes]
rs56370923	0.81[ASN][1000 genomes]
rs58297632	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58945504	0.80[AMR][1000 genomes]
rs59289255	0.96[ASN][1000 genomes]
rs59352354	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60216585	0.81[ASN][1000 genomes]
rs60336404	0.81[ASN][1000 genomes]
rs61442465	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66487782	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66780758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66805306	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66927787	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66942309	0.83[ASN][1000 genomes]
rs67204670	0.83[ASN][1000 genomes]
rs67317524	0.81[ASN][1000 genomes]
rs67349960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67600689	0.81[ASN][1000 genomes]
rs6762272	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6766480	0.89[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs67784045	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778879	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs68056570	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809764	0.84[ASN][1000 genomes]
rs72611188	0.99[ASN][1000 genomes]
rs73212160	0.81[ASN][1000 genomes]
rs73212178	0.83[ASN][1000 genomes]
rs7625886	0.85[JPT][hapmap]
rs7636149	0.81[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639752	0.85[JPT][hapmap]
rs7640304	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870339	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs939883	0.85[JPT][hapmap]
rs9714038	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2088666	OSTalpha	cis	cerebellum	SCAN
rs2088666	TCTEX1D2	cis	parietal	SCAN
rs2088666	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:195996600-196012600	Weak transcription	Fetal Kidney	kidney
5	chr3:195997600-196010600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:196000600-196011200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:196000600-196012400	Weak transcription	Fetal Brain Female	brain
8	chr3:196000600-196012600	Weak transcription	Fetal Lung	lung
9	chr3:196000600-196012800	Weak transcription	Ovary	ovary
10	chr3:196000600-196013800	Weak transcription	Aorta	Aorta
11	chr3:196001000-196011600	Weak transcription	Thymus	Thymus
12	chr3:196001000-196013800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:196001200-196011400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:196001200-196013600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:196001400-196013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:196001400-196013200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:196001600-196013000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:196001800-196010600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:196001800-196011600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:196001800-196012600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:196001800-196012600	Weak transcription	Fetal Stomach	stomach
22	chr3:196002000-196011600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:196002200-196011800	Weak transcription	Dnd41	blood
24	chr3:196002200-196012600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:196002400-196011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:196002400-196012600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:196005000-196011200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:196005000-196013000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:196005600-196012400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:196005800-196012000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:196006000-196012800	Enhancers	Fetal Intestine Small	intestine
32	chr3:196006000-196013000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:196006400-196011400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:196006400-196011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:196006400-196011800	Weak transcription	Primary B cells from cord blood	blood
36	chr3:196006400-196013000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:196006600-196010600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:196006600-196010600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:196006600-196010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:196006600-196010600	Weak transcription	NHLF	lung
41	chr3:196006600-196010800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:196006600-196011000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:196006600-196011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:196006600-196011400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:196006600-196011400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:196006600-196011400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:196006600-196011400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:196006600-196011400	Weak transcription	Placenta	Placenta
49	chr3:196006600-196012400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:196006600-196012600	Weak transcription	Colonic Mucosa	Colon

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