Variant report

Variant	rs1995939
Chromosome Location	chr15:43012517-43012518
allele	A/G
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	chr15:43007397..43009798-chr15:43011681..43013458,2	MCF-7	breast:
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: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10162939	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10400824	0.86[EUR][1000 genomes]
rs11070374	1.00[YRI][hapmap]
rs1197548	0.83[EUR][1000 genomes]
rs1197549	0.83[EUR][1000 genomes]
rs1197550	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1197551	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1206698	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12102055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594483	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12594855	0.94[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12594951	0.87[ASW][hapmap]
rs12903762	0.81[EUR][1000 genomes]
rs12905385	0.90[CEU][hapmap]
rs12905592	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12906497	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907826	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912064	0.94[EUR][1000 genomes]
rs12914570	0.85[CEU][hapmap]
rs12917018	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12917189	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16957020	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs16957091	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16957104	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1705356	0.85[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1915241	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136899	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2136900	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2136901	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305084	0.85[CEU][hapmap];0.85[MEX][hapmap];0.91[EUR][1000 genomes]
rs2305085	0.82[CEU][hapmap]
rs2412740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412741	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28479391	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28549876	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28562951	0.93[EUR][1000 genomes]
rs28744617	0.81[EUR][1000 genomes]
rs28798437	0.86[EUR][1000 genomes]
rs28811114	0.85[EUR][1000 genomes]
rs28823029	0.85[EUR][1000 genomes]
rs3099758	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs3199486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34191150	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35616173	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35738819	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3742987	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742988	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4265781	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923950	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4924690	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924691	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4924694	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4994112	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap]
rs58938096	0.81[EUR][1000 genomes]
rs623271	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6493059	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs6493060	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs6493061	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493062	0.82[AMR][1000 genomes]
rs6493063	0.91[EUR][1000 genomes]
rs6493066	0.84[EUR][1000 genomes]
rs6493067	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6493068	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs67391479	0.91[EUR][1000 genomes]
rs7163030	0.90[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7166373	0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7166632	0.81[EUR][1000 genomes]
rs7166775	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167392	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs7167802	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap]
rs7169009	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169202	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174041	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7175582	0.85[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs7176860	0.81[EUR][1000 genomes]
rs7182141	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs7182479	0.83[EUR][1000 genomes]
rs7182753	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7183487	0.81[EUR][1000 genomes]
rs731984	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023524	0.90[CEU][hapmap]
rs8026233	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027427	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030587	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs8031218	0.81[GIH][hapmap]
rs8034447	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034664	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8035752	1.00[ASW][hapmap]
rs8036096	1.00[ASW][hapmap]
rs8039765	0.85[GIH][hapmap]
rs8043472	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9269	0.95[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs9783683	1.00[YRI][hapmap]
rs9783713	0.94[EUR][1000 genomes]
rs9806175	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs9919994	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs9920163	0.85[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs9920182	0.94[JPT][hapmap];0.85[MEX][hapmap]
rs9944248	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]

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
rs1995939	CDAN1	cis	parietal	SCAN
rs1995939	SPTBN5	cis	cerebellum	SCAN
rs1995939	TGM5	cis	lymphoblastoid	seeQTL
rs1995939	BUB1B	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
4	chr15:42981400-43015000	Weak transcription	HSMM	muscle
5	chr15:42984000-43014800	Weak transcription	K562	blood
6	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:42987800-43016400	Weak transcription	Esophagus	oesophagus
8	chr15:42993400-43015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:42997200-43016400	Weak transcription	Pancreas	Pancrea
10	chr15:43000800-43018600	Weak transcription	A549	lung
11	chr15:43001000-43014800	Weak transcription	HUVEC	blood vessel
12	chr15:43004200-43016200	Weak transcription	Psoas Muscle	Psoas
13	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
14	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:43008000-43014000	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:43008200-43013000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
22	chr15:43008600-43012800	Strong transcription	Brain Cingulate Gyrus	brain
23	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
24	chr15:43008800-43012600	Strong transcription	Aorta	Aorta
25	chr15:43008800-43014000	Strong transcription	Rectal Smooth Muscle	rectum
26	chr15:43008800-43014200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:43008800-43017200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:43008800-43018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
32	chr15:43008800-43027200	Strong transcription	Lung	lung
33	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
34	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:43009000-43012800	Strong transcription	Brain Hippocampus Middle	brain
36	chr15:43009000-43012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:43009000-43013400	Strong transcription	Right Ventricle	heart
38	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
41	chr15:43009200-43012600	Weak transcription	Dnd41	blood
42	chr15:43009200-43013000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:43009200-43014800	Weak transcription	Osteobl	bone
44	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:43009400-43015200	Weak transcription	NHDF-Ad	bronchial
46	chr15:43009400-43015600	Weak transcription	Small Intestine	intestine
47	chr15:43009400-43017400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:43009400-43018200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
50	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine

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