Variant report

Variant	rs1017996
Chromosome Location	chr5:79269697-79269698
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79269309..79272565-chr5:79276555..79279232,3	MCF-7	breast:
2	chr5:79262485..79266204-chr5:79269459..79273570,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10035728	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10041212	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10041404	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10043116	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10060444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap]
rs10065778	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10066471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10071601	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10077238	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1017997	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1017998	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1032341	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1032342	0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11741143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11748289	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13354864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1438739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404708	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451929	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451930	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2471104	1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs2471105	0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2471107	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2471108	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2471109	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs405878	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs422690	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6453494	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6453495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6860568	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865678	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868916	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6870377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873684	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6882768	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6887873	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6892826	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7446065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7707036	0.80[ASN][1000 genomes]
rs7734858	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs923634	0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs923636	0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9293795	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs963423	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs963424	0.85[AMR][1000 genomes];0.84[EUR][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	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1017996	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79259200-79270800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:79259400-79271400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:79259400-79272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:79260600-79286200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:79263200-79273200	Weak transcription	Psoas Muscle	Psoas
6	chr5:79265800-79270800	Weak transcription	Left Ventricle	heart
7	chr5:79266600-79271000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:79267000-79270400	Weak transcription	Adipose Nuclei	Adipose
9	chr5:79267000-79271000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:79267200-79270600	Weak transcription	Osteobl	bone
11	chr5:79267400-79270000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:79267400-79270000	Weak transcription	HMEC	breast
13	chr5:79267400-79270400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:79267400-79270400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:79267400-79270800	Weak transcription	HUVEC	blood vessel
16	chr5:79267400-79271000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:79267400-79271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr5:79267400-79272600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:79267400-79272800	Weak transcription	Fetal Brain Female	brain
20	chr5:79267600-79269800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:79267600-79269800	Weak transcription	NHEK	skin
22	chr5:79267600-79269800	Weak transcription	NHLF	lung
23	chr5:79267600-79272600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:79267600-79273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:79267800-79273600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:79268000-79270800	Weak transcription	Liver	Liver
27	chr5:79268000-79271000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:79268000-79271200	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:79268000-79273000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:79268000-79273000	Weak transcription	Fetal Intestine Large	intestine
31	chr5:79268000-79273800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:79268200-79271600	Enhancers	NHDF-Ad	bronchial
33	chr5:79268200-79273000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:79268200-79273000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:79268200-79273000	Weak transcription	GM12878-XiMat	blood
36	chr5:79268400-79270000	Weak transcription	Primary B cells from cord blood	blood
37	chr5:79268400-79270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:79268400-79270800	Weak transcription	Primary T cells from cord blood	blood
39	chr5:79268400-79273600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:79268600-79271000	Weak transcription	Fetal Thymus	thymus
41	chr5:79268600-79271200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:79268600-79273000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:79268800-79270600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:79268800-79271000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:79269000-79270400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:79269000-79270800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:79269000-79271600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:79269000-79272800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr5:79269000-79273000	Weak transcription	Aorta	Aorta
50	chr5:79269000-79273000	Weak transcription	Fetal Lung	lung

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