Variant report

Variant	rs6873998
Chromosome Location	chr5:74046656-74046657
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	chr5:74040354..74042046-chr5:74045118..74047151,2	MCF-7	breast:
3	chr5:74046364..74048358-chr5:74051691..74053651,2	MCF-7	breast:
4	chr5:74034327..74035890-chr5:74046348..74047892,2	K562	blood:
5	chr5:74040810..74043898-chr5:74045296..74047358,3	K562	blood:
6	chr5:74040810..74043802-chr5:74045296..74047358,2	K562	blood:

Variant related genes	Relation type
ENSG00000164347	Chromatin interaction
ENSG00000164346	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1048167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	0.93[ASW][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11742773	0.89[AFR][1000 genomes]
rs11749137	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11959570	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350097	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs2061162	1.00[YRI][hapmap]
rs2084116	0.89[AFR][1000 genomes]
rs2084118	0.89[AFR][1000 genomes]
rs2100033	0.89[AFR][1000 genomes]
rs3733794	0.93[ASW][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs55899032	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56203772	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57202395	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549677	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58864890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60663580	0.90[AFR][1000 genomes]
rs62366414	0.90[AFR][1000 genomes]
rs62366423	0.84[AFR][1000 genomes]
rs62366426	0.83[AFR][1000 genomes]
rs6453076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877442	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6881400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882499	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6883061	0.93[ASW][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6883278	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884843	0.93[ASW][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs6885675	0.89[AFR][1000 genomes]
rs6894177	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897698	0.83[AFR][1000 genomes]
rs6897904	0.83[AFR][1000 genomes]
rs6898684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764630	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764643	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764657	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728889	1.00[YRI][hapmap]
rs7732440	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686657	0.93[ASW][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6873998	NSA2	cis	Muscle Skeletal	GTEx
rs6873998	NSA2	cis	lymphoblastoid	seeQTL
rs6873998	NSA2	cis	Artery Aorta	GTEx
rs6873998	NSA2	cis	lung	GTEx
rs6873998	TINP1	cis	normal skin	skin_eQTL
rs6873998	NSA2	cis	Esophagus Mucosa	GTEx
rs6873998	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs6873998	NSA2	cis	Esophagus Muscularis	GTEx
rs6873998	NSA2	cis	Nerve Tibial	GTEx
rs6873998	NSA2	cis	Whole Blood	GTEx
rs6873998	NSA2	cis	Adipose Subcutaneous	GTEx
rs6873998	NSA2	cis	Thyroid	GTEx
rs6873998	NSA2	cis	Stomach	GTEx
rs6873998	TINP1	cis	lesional skin	skin_eQTL
rs6873998	NSA2	cis	Artery Tibial	GTEx
rs6873998	NSA2	cis	Heart Left Ventricle	GTEx
rs6873998	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs6873998	TINP1	cis	multi-tissue	Pritchard
rs6873998	TINP1	cis	uninvolved skin	skin_eQTL

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	chr5:74013400-74047400	Strong transcription	Adipose Nuclei	Adipose
14	chr5:74014400-74047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:74014400-74051600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:74015200-74048600	Weak transcription	Stomach Mucosa	stomach
17	chr5:74016400-74052400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:74018000-74060800	Weak transcription	Gastric	stomach
19	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:74018800-74049000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:74019200-74058600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
23	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:74022800-74052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:74023400-74047600	Strong transcription	Fetal Thymus	thymus
26	chr5:74023800-74048600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:74024200-74049400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
29	chr5:74027400-74052000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:74029600-74052200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:74031800-74052600	Weak transcription	Small Intestine	intestine
32	chr5:74032000-74054200	Weak transcription	Lung	lung
33	chr5:74033800-74053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:74037000-74049600	Strong transcription	HSMM	muscle
35	chr5:74037400-74047400	Strong transcription	Primary B cells from cord blood	blood
36	chr5:74037400-74047600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:74037400-74047800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:74037600-74047600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:74037600-74047800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:74037800-74049400	Strong transcription	Liver	Liver
41	chr5:74038000-74049200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:74038000-74052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:74038400-74047400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr5:74038800-74047400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:74038800-74047400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:74038800-74047400	Strong transcription	NH-A	brain
47	chr5:74039200-74047400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr5:74039200-74047400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:74039200-74047400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:74039200-74047800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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