Variant report

Variant	rs10175486
Chromosome Location	chr2:20109061-20109062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20100918..20104038-chr2:20105994..20109592,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10175236	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190645	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10203067	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211513	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11096633	0.94[CEU][hapmap];0.84[GIH][hapmap]
rs1147110	0.94[CEU][hapmap]
rs11887799	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12328613	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12467740	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478941	1.00[CEU][hapmap]
rs12615824	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1462754	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16987206	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987297	1.00[CEU][hapmap]
rs2278528	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304589	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28742930	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754907	0.82[CEU][hapmap]
rs3754908	0.82[CEU][hapmap]
rs3769763	0.82[CEU][hapmap]
rs58978345	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6716854	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717139	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721754	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757734	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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	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	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
4	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
5	nsv522640	chr2:20098208-20109061	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10175486	TTC32	cis	lymphoblastoid	seeQTL
rs10175486	TTC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102200-20113400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:20102200-20116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:20102400-20111600	Weak transcription	Ovary	ovary
4	chr2:20102400-20126600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:20102600-20111000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:20102600-20113400	Weak transcription	Thymus	Thymus
7	chr2:20102600-20115800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:20102600-20115800	Weak transcription	Fetal Stomach	stomach
9	chr2:20102600-20119000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:20102600-20127600	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:20102600-20127800	Weak transcription	Aorta	Aorta
12	chr2:20102600-20128000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:20102800-20110800	Weak transcription	NH-A	brain
14	chr2:20102800-20111000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:20102800-20111200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:20102800-20111400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:20102800-20113200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:20102800-20113200	Weak transcription	HepG2	liver
19	chr2:20102800-20115600	Weak transcription	Fetal Intestine Small	intestine
20	chr2:20102800-20115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:20102800-20116000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:20102800-20123200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:20102800-20123600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:20102800-20126600	Weak transcription	Adipose Nuclei	Adipose
25	chr2:20102800-20126600	Weak transcription	Fetal Lung	lung
26	chr2:20102800-20126800	Weak transcription	Fetal Kidney	kidney
27	chr2:20102800-20127200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:20102800-20127600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:20102800-20127600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:20102800-20128800	Weak transcription	Liver	Liver
31	chr2:20102800-20128800	Weak transcription	Brain Germinal Matrix	brain
32	chr2:20102800-20129000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
34	chr2:20103000-20113200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:20103000-20116200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:20103000-20126800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:20103000-20127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:20103200-20110200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:20103200-20111000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:20103200-20111000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:20103200-20111000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:20103200-20111600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:20103200-20112000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:20103400-20110400	Weak transcription	A549	lung
45	chr2:20103400-20110600	Weak transcription	NHDF-Ad	bronchial
46	chr2:20103400-20111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:20103600-20110400	Weak transcription	HSMM	muscle
48	chr2:20103600-20111000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:20105000-20127400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:20105400-20129000	Weak transcription	Primary T cells from cord blood	blood

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