Variant report

Variant	rs2295504
Chromosome Location	chr20:13593846-13593847
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13591529..13593880-chr20:13614121..13615856,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1040756	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs11087055	0.84[ASN][1000 genomes]
rs13040087	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057259	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2070307	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs2070308	0.94[LWK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs2070334	0.80[ASW][hapmap]
rs2180569	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2295503	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2327793	0.88[ASN][1000 genomes]
rs2423729	0.92[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs2423730	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs2423731	0.84[AFR][1000 genomes]
rs2423732	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2423733	0.94[ASN][1000 genomes]
rs2423734	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2423736	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2423737	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423738	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2423739	0.87[ASN][1000 genomes]
rs34146992	0.97[ASN][1000 genomes]
rs34822601	0.85[ASN][1000 genomes]
rs4303776	0.84[ASN][1000 genomes]
rs4441543	0.86[ASN][1000 genomes]
rs6033766	0.97[ASN][1000 genomes]
rs6033767	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033768	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs6033773	0.87[AFR][1000 genomes]
rs6033777	0.87[LWK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs6033783	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033793	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033795	0.92[ASN][1000 genomes]
rs6042106	0.80[ASW][hapmap]
rs6042225	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042235	0.87[ASN][1000 genomes]
rs6042236	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs6042239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6042240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6042255	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs6042263	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs6042264	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042266	0.85[AFR][1000 genomes]
rs6042273	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042285	0.88[ASN][1000 genomes]
rs6042301	0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6105137	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105142	0.87[AFR][1000 genomes]
rs6109979	0.87[AFR][1000 genomes]
rs6109983	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109990	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109993	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109995	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6131499	0.85[ASN][1000 genomes]
rs6134919	0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6134930	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs6134935	0.97[ASN][1000 genomes]
rs6134948	0.93[ASN][1000 genomes]
rs6514418	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1797514	chr20:13541011-13610424	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS 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	4 gene(s)	inside rSNPs	diseases
7	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2295504	C20orf94	cis	cerebellum	SCAN
rs2295504	MKKS	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
3	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:13564000-13602600	Weak transcription	Ovary	ovary
8	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
9	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr20:13564200-13608400	Weak transcription	HSMM	muscle
12	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
14	chr20:13567400-13594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:13567400-13597400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:13567400-13602800	Weak transcription	A549	lung
17	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:13567400-13608400	Weak transcription	HMEC	breast
20	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr20:13568800-13602800	Weak transcription	Fetal Intestine Large	intestine
24	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:13574200-13606600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr20:13574400-13606400	Weak transcription	Thymus	Thymus
28	chr20:13574600-13606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:13581000-13595800	Weak transcription	NHEK	skin
30	chr20:13581200-13606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr20:13582000-13603000	Weak transcription	Liver	Liver
32	chr20:13582200-13606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr20:13582600-13608000	Weak transcription	HSMMtube	muscle
34	chr20:13583200-13602800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:13583200-13607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr20:13583200-13607200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr20:13583400-13607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr20:13583800-13605400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
40	chr20:13584200-13594600	Weak transcription	Fetal Stomach	stomach
41	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas
42	chr20:13585200-13602800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr20:13585200-13609000	Weak transcription	Fetal Muscle Leg	muscle
44	chr20:13585600-13594000	Weak transcription	Brain Germinal Matrix	brain
45	chr20:13585600-13594600	Weak transcription	Fetal Lung	lung
46	chr20:13585600-13606400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:13586200-13602400	Weak transcription	Fetal Kidney	kidney
48	chr20:13586400-13598600	Weak transcription	Fetal Intestine Small	intestine
49	chr20:13586600-13608600	Weak transcription	GM12878-XiMat	blood
50	chr20:13587000-13597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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