Variant report

Variant	rs16987206
Chromosome Location	chr2:20090739-20090740
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	chr2:20089099..20091154-chr2:20092345..20094469,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10175236	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10175486	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10190645	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10203067	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10211513	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11096633	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs1147110	0.88[CEU][hapmap]
rs11887799	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467740	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12478941	0.94[CEU][hapmap]
rs12615824	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1462754	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16987297	0.94[CEU][hapmap]
rs2278528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28742930	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754907	0.87[CEU][hapmap]
rs3754908	0.87[CEU][hapmap]
rs3769763	0.87[CEU][hapmap]
rs6716854	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717139	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721754	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised 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	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16987206	TTC32	cis	lymphoblastoid	seeQTL
rs16987206	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs16987206	TTC32	cis	cerebellum	SCAN
rs16987206	LOC130502	cis	multi-tissue	Pritchard
rs16987206	TTC32	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
2	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
3	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
5	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
13	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:20079400-20097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
18	chr2:20081800-20095200	Weak transcription	Primary T cells from cord blood	blood
19	chr2:20083000-20095400	Weak transcription	Fetal Brain Female	brain
20	chr2:20086400-20097400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:20086600-20091200	Weak transcription	Psoas Muscle	Psoas
22	chr2:20086600-20091800	Weak transcription	Spleen	Spleen
23	chr2:20086600-20095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:20086600-20097400	Weak transcription	HMEC	breast
25	chr2:20086600-20099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:20087200-20097400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:20087400-20097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:20088000-20091200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:20088000-20099600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:20088400-20090800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:20088400-20098200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:20088800-20091800	Weak transcription	Fetal Brain Male	brain
33	chr2:20089000-20095200	Weak transcription	Dnd41	blood
34	chr2:20089000-20097200	Weak transcription	Adipose Nuclei	Adipose
35	chr2:20089200-20097200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:20089200-20097400	Weak transcription	Brain Anterior Caudate	brain
37	chr2:20089400-20097000	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:20089400-20097200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:20089600-20090800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:20089600-20090800	Enhancers	HepG2	liver
41	chr2:20089600-20094200	Weak transcription	K562	blood
42	chr2:20089600-20097200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:20089600-20097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:20089600-20097400	Weak transcription	NHEK	skin
45	chr2:20089600-20097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:20089600-20098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:20089800-20091800	Enhancers	GM12878-XiMat	blood
48	chr2:20089800-20092800	Weak transcription	NHDF-Ad	bronchial
49	chr2:20089800-20095400	Weak transcription	Brain Angular Gyrus	brain
50	chr2:20089800-20095600	Weak transcription	Osteobl	bone

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