Variant report

Variant	rs9308669
Chromosome Location	chr2:112864369-112864370
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112858852..112860366-chr2:112864135..112866209,2	K562	blood:
2	chr2:112849351..112852344-chr2:112862673..112866041,3	MCF-7	breast:
3	chr2:112856304..112858308-chr2:112863818..112865779,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10165845	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175143	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178449	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182333	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045300	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779884	0.97[ASN][1000 genomes]
rs10864898	0.88[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618637	0.90[ASN][1000 genomes]
rs4241121	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257409	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4848993	0.82[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849007	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849044	0.90[ASN][1000 genomes]
rs6707397	0.85[CEU][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6730057	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731563	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737707	0.83[MEX][hapmap]
rs7577442	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580507	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581849	0.90[JPT][hapmap]
rs7591702	0.82[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595574	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653401	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653422	0.92[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9308669	MERTK	cis	multi-tissue	Pritchard
rs9308669	FBLN7	cis	cerebellum	SCAN
rs9308669	POLR1B	cis	cerebellum	SCAN
rs9308669	POLR1B	cis	parietal	SCAN
rs9308669	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:112832000-112866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:112834600-112871200	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:112836000-112874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:112838200-112866200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:112838200-112866400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr2:112843000-112869400	Weak transcription	Fetal Heart	heart
11	chr2:112845400-112875200	Weak transcription	Right Ventricle	heart
12	chr2:112845600-112865400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:112846200-112865800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:112847800-112867200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:112851000-112866400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:112851000-112867600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:112851200-112881600	Weak transcription	Stomach Mucosa	stomach
18	chr2:112852000-112871200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:112852800-112866000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:112853200-112864600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:112853200-112865600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:112853200-112866000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:112853200-112866200	Strong transcription	Liver	Liver
24	chr2:112853200-112866600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:112853200-112871200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr2:112853200-112871200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:112853400-112865600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:112853400-112866200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:112853400-112866400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:112853400-112871200	Strong transcription	Placenta	Placenta
31	chr2:112854200-112865600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:112854200-112866200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:112854400-112865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:112854400-112869400	Weak transcription	Esophagus	oesophagus
35	chr2:112855200-112866000	Weak transcription	Psoas Muscle	Psoas
36	chr2:112855400-112871200	Strong transcription	NH-A	brain
37	chr2:112855800-112867200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:112856000-112866200	Strong transcription	Primary B cells from cord blood	blood
39	chr2:112856000-112866600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:112856800-112865200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:112856800-112865800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:112856800-112866000	Weak transcription	Brain Anterior Caudate	brain
43	chr2:112856800-112866400	Weak transcription	Fetal Brain Male	brain
44	chr2:112856800-112869400	Weak transcription	Aorta	Aorta
45	chr2:112856800-112869400	Weak transcription	Gastric	stomach
46	chr2:112856800-112869400	Weak transcription	Pancreas	Pancrea
47	chr2:112856800-112869400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:112856800-112869400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:112856800-112870200	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:112856800-112874200	Weak transcription	Lung	lung

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