Variant report

Variant	rs2136899
Chromosome Location	chr15:42990386-42990387
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	chr15:42983549..42985784-chr15:42989459..42991340,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10162939	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10518779	1.00[JPT][hapmap]
rs1058846	0.94[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs11638835	0.80[EUR][1000 genomes]
rs1197550	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1197551	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12102055	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12594855	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12902830	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs12903762	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12905385	0.93[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12905592	0.88[EUR][1000 genomes]
rs12906497	0.80[CEU][hapmap]
rs12907826	0.89[EUR][1000 genomes]
rs12911585	0.89[CEU][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs12913618	0.83[EUR][1000 genomes]
rs12914570	0.85[ASW][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap]
rs12915116	0.84[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs12917189	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs16957020	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[YRI][hapmap]
rs16957043	0.89[YRI][hapmap]
rs16957168	0.86[ASW][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1705356	0.90[JPT][hapmap]
rs17774047	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1995939	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2136900	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136901	0.92[EUR][1000 genomes]
rs2175370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280048	0.84[CEU][hapmap]
rs2305084	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305085	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412741	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs28498538	0.90[ASN][1000 genomes]
rs28562951	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620320	0.85[ASN][1000 genomes]
rs28664781	0.83[ASN][1000 genomes]
rs28744617	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3099758	0.90[JPT][hapmap]
rs3199486	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs34070722	0.86[EUR][1000 genomes]
rs34191150	0.92[EUR][1000 genomes]
rs34603230	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35088691	0.82[EUR][1000 genomes]
rs35298309	0.80[EUR][1000 genomes]
rs35392023	0.91[EUR][1000 genomes]
rs35538776	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs35616173	0.92[EUR][1000 genomes]
rs35738819	0.87[EUR][1000 genomes]
rs3742988	0.85[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs3742993	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545789	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923950	0.86[EUR][1000 genomes]
rs4924691	1.00[CHB][hapmap]
rs4924692	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4994112	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs57298545	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58938096	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61122145	0.92[EUR][1000 genomes]
rs623271	0.90[JPT][hapmap]
rs6493059	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6493060	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6493061	0.94[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6493062	0.91[EUR][1000 genomes]
rs6493063	0.83[ASN][1000 genomes]
rs6493066	0.83[ASN][1000 genomes]
rs66681258	0.92[EUR][1000 genomes]
rs672054	0.89[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs71474496	0.84[EUR][1000 genomes]
rs7166373	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7167392	0.80[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7169009	0.85[CEU][hapmap]
rs7174041	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs7175582	0.80[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176860	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182141	0.86[ASW][hapmap];0.80[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7182479	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7182515	1.00[JPT][hapmap]
rs7183487	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs731984	0.85[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs8023524	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8024902	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028785	1.00[JPT][hapmap]
rs8030587	0.83[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs8031218	0.83[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8034447	0.85[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs8039711	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039765	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9269	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938047	0.89[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9783713	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9919994	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9920163	0.81[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9920202	1.00[JPT][hapmap]
rs9944248	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv1812752	chr15:42988175-42994169	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3311736	chr15:42988779-42995374	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3311737	chr15:42988779-42995374	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv15854	chr15:42989012-42995070	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2763096	chr15:42989603-43009399	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2136899	CDAN1	cis	parietal	SCAN
rs2136899	BUB1B	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42949800-42999200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:42951000-42995000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr15:42952600-42995600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:42952800-42996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:42953400-42992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42961400-42990800	Strong transcription	Colon Smooth Muscle	Colon
8	chr15:42966000-42992800	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:42968400-42992200	Weak transcription	Fetal Brain Male	brain
10	chr15:42968600-42996800	Weak transcription	Liver	Liver
11	chr15:42968600-42999000	Weak transcription	HUVEC	blood vessel
12	chr15:42971400-42992600	Strong transcription	Adipose Nuclei	Adipose
13	chr15:42971600-42992400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:42973200-42991200	Strong transcription	Brain Germinal Matrix	brain
15	chr15:42973600-42992600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:42975600-43011400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:42976600-42990400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:42976600-42992200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:42976600-42996800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:42976600-43015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:42977000-42999400	Weak transcription	HepG2	liver
22	chr15:42977000-43011600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
24	chr15:42978200-42996800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:42978200-43010400	Weak transcription	Thymus	Thymus
26	chr15:42978400-42991000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:42978600-42992400	Weak transcription	Small Intestine	intestine
28	chr15:42978800-43012000	Weak transcription	NH-A	brain
29	chr15:42979000-42992600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:42979200-42992400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:42979200-43011000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:42979600-43010000	Weak transcription	GM12878-XiMat	blood
33	chr15:42979800-43010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:42980200-43002800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:42980400-43010400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:42980800-42992400	Weak transcription	Fetal Heart	heart
37	chr15:42981400-42999400	Weak transcription	HMEC	breast
38	chr15:42981400-43015000	Weak transcription	HSMM	muscle
39	chr15:42981600-42999400	Weak transcription	NHEK	skin
40	chr15:42981600-43009800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:42981600-43011000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:42981800-43010000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:42982000-42999400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:42983800-42990400	Strong transcription	Fetal Brain Female	brain
45	chr15:42984000-42995800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:42984000-43014800	Weak transcription	K562	blood
47	chr15:42985200-42992000	Weak transcription	Fetal Lung	lung
48	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:42987000-42990400	Strong transcription	Primary B cells from cord blood	blood
50	chr15:42987200-43010000	Weak transcription	Rectal Mucosa Donor 29	rectum

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