Variant report

Variant	rs10049060
Chromosome Location	chr3:121358448-121358449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1127412	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1128163	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11916169	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12634032	1.00[CEU][hapmap]
rs12635865	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1463736	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574115	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1574133	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2141487	1.00[CEU][hapmap]
rs3732407	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3732410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4048699	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4048703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58367397	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6771068	1.00[CEU][hapmap]
rs6791882	0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7153	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610298	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623901	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs7647351	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648340	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648343	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9808981	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9810952	0.80[CHD][hapmap]
rs9817818	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818073	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9820511	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824235	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9824760	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9838301	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850439	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9852845	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874722	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
6	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10049060	SLC15A2	cis	cerebellum	SCAN
rs10049060	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs10049060	IQCB1	cis	parietal	SCAN
rs10049060	GOLGB1	cis	multi-tissue	Pritchard
rs10049060	EAF2	cis	lymphoblastoid	seeQTL
rs10049060	EAF2	cis	cerebellum	SCAN
rs10049060	STAM2	trans	lymphoblastoid	RTeQTL
rs10049060	ALG1L	cis	parietal	SCAN
rs10049060	IQCB1	cis	cerebellum	SCAN
rs10049060	IQCB1	cis	lymphoblastoid	seeQTL
rs10049060	EAF2	cis	multi-tissue	Pritchard
rs10049060	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs10049060	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
2	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
3	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
4	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:121347600-121359400	Strong transcription	Primary T cells from cord blood	blood
6	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:121348000-121364600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:121348000-121364600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
13	chr3:121348200-121364600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:121348400-121364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:121348400-121364600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:121348800-121358600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:121348800-121363000	Weak transcription	Left Ventricle	heart
18	chr3:121348800-121364400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:121348800-121367200	Weak transcription	Pancreas	Pancrea
20	chr3:121349000-121359000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr3:121349000-121364600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:121349000-121364600	Strong transcription	Dnd41	blood
23	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
24	chr3:121349200-121359200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:121349200-121362000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:121349200-121364200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:121349400-121364600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:121349400-121367000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:121349600-121358600	Strong transcription	Thymus	Thymus
30	chr3:121349600-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:121349800-121359400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:121349800-121367000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:121350000-121364600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:121350000-121364600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:121351000-121364600	Strong transcription	GM12878-XiMat	blood
36	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
37	chr3:121351400-121381400	Weak transcription	Gastric	stomach
38	chr3:121351600-121360800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:121351800-121358600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:121351800-121370400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:121353400-121364400	Strong transcription	Fetal Thymus	thymus
42	chr3:121353400-121376000	Weak transcription	Lung	lung
43	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
44	chr3:121354400-121361600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:121355600-121367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:121355800-121361400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:121356000-121370200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:121356200-121378200	Weak transcription	Colonic Mucosa	Colon
49	chr3:121356400-121360200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:121356800-121362000	Weak transcription	Duodenum Mucosa	Duodenum

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