Variant report

Variant	rs3768648
Chromosome Location	chr2:153003412-153003413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152995687..152997718-chr2:153000846..153003474,2	K562	blood:
2	chr2:152995292..152997762-chr2:153001457..153003631,2	K562	blood:
3	chr2:152998723..153001104-chr2:153002092..153003596,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10177222	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187630	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203659	0.82[ASW][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap]
rs10469642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497095	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497097	0.84[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10803946	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs10930923	0.93[GIH][hapmap];0.90[MEX][hapmap]
rs10930939	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930959	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133478	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11694120	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11884659	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11893841	0.95[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12328733	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12468532	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12472524	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476550	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612557	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613984	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615156	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621378	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622092	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623355	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693270	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693271	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13003423	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13424583	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2002247	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28785043	0.82[AMR][1000 genomes]
rs34233450	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35155943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35717822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768649	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768651	0.84[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806464	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4255959	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4368329	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4473376	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4505521	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4611639	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664080	0.85[ASN][1000 genomes]
rs4664084	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664085	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4664089	0.89[CEU][hapmap];0.84[LWK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap]
rs4664530	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664531	0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4664532	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664535	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664537	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62176474	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62176476	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62176478	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62176479	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650779	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6720552	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71417204	0.83[ASN][1000 genomes]
rs7420277	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7572616	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7588906	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8179814	0.81[AMR][1000 genomes]
rs9917198	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768648	STAM2	cis	lymphoblastoid	seeQTL
rs3768648	STAM2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152971200-153008400	Weak transcription	Esophagus	oesophagus
2	chr2:152974200-153017000	Weak transcription	Colonic Mucosa	Colon
3	chr2:152974800-153003800	Weak transcription	NHEK	skin
4	chr2:152974800-153008200	Weak transcription	Fetal Brain Female	brain
5	chr2:152975000-153003600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:152975000-153005400	Weak transcription	Brain Germinal Matrix	brain
7	chr2:152976000-153014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:152976200-153010200	Weak transcription	Fetal Brain Male	brain
9	chr2:152976200-153013400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:152976400-153005000	Weak transcription	Fetal Heart	heart
11	chr2:152976400-153013400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:152977400-153006200	Weak transcription	HMEC	breast
13	chr2:152978200-153021400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:152981800-153024800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:152982400-153013400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:152983800-153013400	Weak transcription	Psoas Muscle	Psoas
17	chr2:152988400-153007400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:152991600-153010600	Weak transcription	Gastric	stomach
19	chr2:152991800-153008600	Weak transcription	NHLF	lung
20	chr2:152991800-153018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:152992000-153008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:152992000-153011600	Weak transcription	Stomach Mucosa	stomach
23	chr2:152992200-153005800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:152993800-153005200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:152995000-153005400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:152995200-153006800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:152995200-153006800	Strong transcription	Liver	Liver
28	chr2:152995400-153004400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:152995400-153004600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:152995800-153004200	Strong transcription	Fetal Intestine Large	intestine
31	chr2:152995800-153005200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:152996000-153004800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:152996000-153004800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:152996200-153013400	Weak transcription	Right Ventricle	heart
35	chr2:152998400-153004600	Strong transcription	Adipose Nuclei	Adipose
36	chr2:152998400-153004600	Strong transcription	Dnd41	blood
37	chr2:152998400-153004800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:152998400-153004800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:152998400-153005000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:152998400-153005200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:152998400-153005400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:152998400-153007400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:152998400-153013200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:152998400-153013400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:152998600-153004400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:152998600-153004600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:152998600-153004800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:152998600-153004800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:152998600-153005200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:152998600-153005400	Strong transcription	Rectal Mucosa Donor 29	rectum

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