Variant report

Variant	rs9919994
Chromosome Location	chr15:43011537-43011538
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43011244..43015007-chr15:43016381..43019349,5	K562	blood:
2	chr15:43004420..43008133-chr15:43008696..43011545,3	K562	blood:
3	chr15:43010693..43013698-chr15:43016416..43019349,5	K562	blood:
4	chr15:43010972..43017152-chr15:43019499..43025146,7	MCF-7	breast:
5	chr15:43011390..43013542-chr15:43022490..43025034,3	K562	blood:

Variant related genes	Relation type
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10162939	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10400824	0.88[EUR][1000 genomes]
rs10518779	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1197548	0.82[EUR][1000 genomes]
rs1197549	0.82[EUR][1000 genomes]
rs1197550	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1197551	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs12102055	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12903762	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905385	0.90[CEU][hapmap]
rs12906497	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs12912064	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12914570	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs12917018	0.90[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs12917189	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs16957020	0.84[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs16957091	0.90[CEU][hapmap];0.89[GIH][hapmap];0.90[EUR][1000 genomes]
rs16957104	0.91[EUR][1000 genomes]
rs16957168	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1705356	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs1915241	0.88[EUR][1000 genomes]
rs1995939	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs2136899	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2136900	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2175370	0.90[JPT][hapmap]
rs2280048	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2305084	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2305085	0.82[CEU][hapmap]
rs2412740	0.94[EUR][1000 genomes]
rs2412741	0.89[CEU][hapmap]
rs28549876	0.89[EUR][1000 genomes]
rs28562951	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28744617	0.83[EUR][1000 genomes]
rs28798437	0.88[EUR][1000 genomes]
rs28811114	0.87[EUR][1000 genomes]
rs28823029	0.87[EUR][1000 genomes]
rs3099758	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs3199486	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs3742987	0.84[CEU][hapmap];0.87[GIH][hapmap];0.90[EUR][1000 genomes]
rs3742988	0.90[CEU][hapmap];0.87[GIH][hapmap]
rs3742993	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4265781	0.89[EUR][1000 genomes]
rs4924690	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4924691	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4924694	0.84[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs4994112	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs57298545	0.84[ASN][1000 genomes]
rs58938096	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623271	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6493059	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493060	0.83[GIH][hapmap]
rs6493061	0.90[CEU][hapmap];0.83[GIH][hapmap]
rs6493062	0.81[EUR][1000 genomes]
rs6493063	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493066	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66681258	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs672054	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs67391479	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7163030	0.90[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7166632	0.81[EUR][1000 genomes]
rs7166775	0.86[EUR][1000 genomes]
rs7167392	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7169009	0.90[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs7169202	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7174041	0.89[CEU][hapmap]
rs7175582	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs7176860	0.84[EUR][1000 genomes]
rs7182141	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs7182515	1.00[JPT][hapmap]
rs7183487	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731984	0.90[CEU][hapmap];0.87[GIH][hapmap]
rs8023524	0.90[CEU][hapmap]
rs8024902	0.90[JPT][hapmap]
rs8026233	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs8027427	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs8028785	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs8030587	0.83[GIH][hapmap]
rs8031218	0.91[GIH][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap]
rs8034447	0.90[CEU][hapmap];0.87[GIH][hapmap]
rs8034664	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8039711	0.90[JPT][hapmap]
rs8039765	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs8043472	0.85[CEU][hapmap];0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs9269	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs938047	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9783713	0.95[EUR][1000 genomes]
rs9920163	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9920182	0.92[MEX][hapmap]
rs9920202	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9919994	SPTBN5	cis	cerebellum	SCAN
rs9919994	CHAC1	cis	parietal	SCAN
rs9919994	CDAN1	cis	parietal	SCAN
rs9919994	BUB1B	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42976600-43015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42977000-43011600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
5	chr15:42978800-43012000	Weak transcription	NH-A	brain
6	chr15:42981400-43015000	Weak transcription	HSMM	muscle
7	chr15:42984000-43014800	Weak transcription	K562	blood
8	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:42987800-43016400	Weak transcription	Esophagus	oesophagus
10	chr15:42989000-43011800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:42993400-43015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:42997200-43016400	Weak transcription	Pancreas	Pancrea
13	chr15:42999800-43011800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:43000800-43018600	Weak transcription	A549	lung
15	chr15:43001000-43014800	Weak transcription	HUVEC	blood vessel
16	chr15:43003200-43011600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:43003200-43012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:43004200-43016200	Weak transcription	Psoas Muscle	Psoas
19	chr15:43006400-43011800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
21	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:43008000-43014000	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:43008200-43013000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
29	chr15:43008600-43012800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
31	chr15:43008800-43012600	Strong transcription	Aorta	Aorta
32	chr15:43008800-43014000	Strong transcription	Rectal Smooth Muscle	rectum
33	chr15:43008800-43014200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:43008800-43017200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:43008800-43018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
39	chr15:43008800-43027200	Strong transcription	Lung	lung
40	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
41	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:43009000-43012800	Strong transcription	Brain Hippocampus Middle	brain
43	chr15:43009000-43012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:43009000-43013400	Strong transcription	Right Ventricle	heart
45	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
48	chr15:43009200-43011600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr15:43009200-43011600	Weak transcription	HSMMtube	muscle
50	chr15:43009200-43012600	Weak transcription	Dnd41	blood

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