Variant report

Variant	rs10137642
Chromosome Location	chr14:72205321-72205322
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	chr14:72191378..72193291-chr14:72204518..72207982,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1005605	0.97[ASN][1000 genomes]
rs10132111	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10139519	1.00[JPT][hapmap]
rs1204988	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204992	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204995	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204996	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204997	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12880188	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1468373	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981588	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2286135	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286136	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784064	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3825719	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4140799	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899398	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7140501	1.00[JPT][hapmap]
rs7142343	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7156313	1.00[JPT][hapmap]
rs7350725	1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs757744	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015004	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672060	0.86[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1047559	chr14:72151736-72282151	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv84708	chr14:72204904-72209070	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10137642	ACOT2	cis	parietal	SCAN
rs10137642	SMOC1	cis	parietal	SCAN
rs10137642	PCNX	cis	cerebellum	SCAN
rs10137642	PCNX	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72182200-72207400	Strong transcription	GM12878-XiMat	blood
2	chr14:72185800-72206200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr14:72187600-72206200	Strong transcription	Dnd41	blood
4	chr14:72187600-72207600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:72187800-72206200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:72188200-72206400	Strong transcription	Primary T cells from cord blood	blood
7	chr14:72188600-72206000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:72188800-72205800	Strong transcription	Fetal Intestine Large	intestine
9	chr14:72188800-72207600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:72189800-72205800	Strong transcription	Fetal Intestine Small	intestine
11	chr14:72189800-72206000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr14:72189800-72206000	Strong transcription	Spleen	Spleen
13	chr14:72189800-72206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:72189800-72206800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr14:72189800-72206800	Strong transcription	Primary B cells from cord blood	blood
16	chr14:72190000-72206000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:72190000-72206000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:72190200-72206000	Strong transcription	Placenta	Placenta
19	chr14:72190600-72214200	Weak transcription	K562	blood
20	chr14:72191400-72206000	Strong transcription	Liver	Liver
21	chr14:72191600-72206000	Strong transcription	Gastric	stomach
22	chr14:72191600-72206000	Strong transcription	Pancreas	Pancrea
23	chr14:72193000-72207200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr14:72194600-72214800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr14:72195000-72205400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:72195000-72206400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:72195200-72205600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:72195200-72206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:72195200-72206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr14:72195200-72206600	Strong transcription	Thymus	Thymus
31	chr14:72195400-72206000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr14:72196000-72205800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr14:72196000-72206000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr14:72196000-72206000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr14:72196000-72206000	Strong transcription	Fetal Thymus	thymus
36	chr14:72196000-72206000	Strong transcription	Lung	lung
37	chr14:72196200-72205600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:72196200-72205600	Strong transcription	NHEK	skin
39	chr14:72196200-72206000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr14:72196200-72206000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:72196200-72206000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr14:72196200-72206000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr14:72196400-72205800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:72196400-72205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr14:72196600-72206000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr14:72197200-72206600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:72200400-72205600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr14:72200400-72206000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:72200400-72206400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr14:72200400-72207200	Strong transcription	Aorta	Aorta

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