Variant report

Variant	rs16872242
Chromosome Location	chr5:74047436-74047437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74045315..74047772-chr5:74062616..74065560,2	MCF-7	breast:
2	chr5:74046364..74048358-chr5:74051691..74053651,2	MCF-7	breast:
3	chr5:74034327..74035890-chr5:74046348..74047892,2	K562	blood:

Variant related genes	Relation type
ENSG00000164346	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1048167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11959570	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs55899032	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56203772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57202395	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549677	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58864890	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	1.00[EUR][1000 genomes]
rs6861935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883278	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894177	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764630	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764643	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764657	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7713812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732440	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs16872242	TINP1	cis	multi-tissue	Pritchard
rs16872242	NSA2	cis	Adipose Subcutaneous	GTEx
rs16872242	NSA2	cis	Esophagus Muscularis	GTEx
rs16872242	NSA2	cis	Muscle Skeletal	GTEx
rs16872242	NSA2	cis	Artery Tibial	GTEx
rs16872242	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs16872242	NSA2	cis	Stomach	GTEx
rs16872242	TINP1	cis	uninvolved skin	skin_eQTL
rs16872242	TINP1	cis	normal skin	skin_eQTL
rs16872242	NSA2	cis	Heart Left Ventricle	GTEx
rs16872242	NSA2	cis	Thyroid	GTEx
rs16872242	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs16872242	NSA2	cis	Nerve Tibial	GTEx
rs16872242	NSA2	cis	Esophagus Mucosa	GTEx
rs16872242	NSA2	cis	Artery Aorta	GTEx
rs16872242	TINP1	cis	lesional skin	skin_eQTL
rs16872242	NSA2	cis	lung	GTEx
rs16872242	NSA2	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
3	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74002600-74051600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:74008400-74047800	Strong transcription	Placenta	Placenta
7	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:74010200-74048000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:74012000-74051600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:74012200-74050400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:74014400-74047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:74014400-74051600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:74015200-74048600	Weak transcription	Stomach Mucosa	stomach
16	chr5:74016400-74052400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:74018000-74060800	Weak transcription	Gastric	stomach
18	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:74018800-74049000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:74019200-74058600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
22	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:74022800-74052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:74023400-74047600	Strong transcription	Fetal Thymus	thymus
25	chr5:74023800-74048600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr5:74024200-74049400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
28	chr5:74027400-74052000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:74029600-74052200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:74031800-74052600	Weak transcription	Small Intestine	intestine
31	chr5:74032000-74054200	Weak transcription	Lung	lung
32	chr5:74033800-74053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:74037000-74049600	Strong transcription	HSMM	muscle
34	chr5:74037400-74047600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:74037400-74047800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:74037600-74047600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:74037600-74047800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:74037800-74049400	Strong transcription	Liver	Liver
39	chr5:74038000-74049200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:74038000-74052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:74039200-74047800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:74039400-74047800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:74039400-74049000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:74039600-74048000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:74039800-74047800	Strong transcription	GM12878-XiMat	blood
46	chr5:74039800-74049400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr5:74040000-74054200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:74041400-74050200	Strong transcription	Fetal Lung	lung
49	chr5:74041800-74047600	Strong transcription	NHDF-Ad	bronchial
50	chr5:74042400-74047600	Strong transcription	Fetal Muscle Leg	muscle

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