Variant report

Variant	rs4729873
Chromosome Location	chr7:102731781-102731782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102714473..102716689-chr7:102731603..102733946,2	MCF-7	breast:
2	chr7:102724877..102726514-chr7:102730311..102733087,2	K562	blood:
3	chr7:102724225..102725917-chr7:102730430..102732210,2	MCF-7	breast:
4	chr7:102731360..102734429-chr7:102788737..102792163,3	K562	blood:

Variant related genes	Relation type
ENSG00000161040	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000161048	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10808120	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs10953380	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953382	0.87[ASN][1000 genomes]
rs10953383	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11514917	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs11768949	0.84[ASN][1000 genomes]
rs11770319	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11972261	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11976237	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12537977	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12666317	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs12667116	0.81[AMR][1000 genomes]
rs13221585	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13221979	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13222980	0.93[ASN][1000 genomes]
rs13229214	0.88[ASN][1000 genomes]
rs13232194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13233521	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs13242493	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs1608651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1829957	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2222539	0.90[ASN][1000 genomes]
rs2298854	0.97[ASN][1000 genomes]
rs4609128	0.88[ASN][1000 genomes]
rs4620204	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs4729860	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4729866	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6947403	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6960428	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs6963104	0.84[TSI][hapmap]
rs6978630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7458786	0.86[ASN][1000 genomes]
rs7780405	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7785272	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7789252	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7796678	0.85[ASN][1000 genomes]
rs7807055	0.88[ASN][1000 genomes]
rs847646	0.91[JPT][hapmap]
rs847647	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs847648	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs847649	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs847656	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs847658	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs869332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs952879	0.86[ASN][1000 genomes]
rs9718453	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv526764	chr7:102701826-102737251	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4729873	LRRC17	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102716400-102734000	Weak transcription	Esophagus	oesophagus
2	chr7:102716400-102745400	Weak transcription	Spleen	Spleen
3	chr7:102716600-102735600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:102716600-102737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:102716600-102746400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:102716600-102746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:102716600-102746800	Weak transcription	Right Atrium	heart
8	chr7:102716600-102760200	Weak transcription	Lung	lung
9	chr7:102716600-102762200	Weak transcription	Colonic Mucosa	Colon
10	chr7:102716600-102768200	Weak transcription	Right Ventricle	heart
11	chr7:102716800-102753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:102716800-102768400	Weak transcription	Stomach Mucosa	stomach
13	chr7:102717000-102746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:102717000-102746800	Weak transcription	Fetal Heart	heart
15	chr7:102717600-102738600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:102717600-102770200	Weak transcription	Small Intestine	intestine
17	chr7:102717800-102768000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:102719400-102769600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:102722200-102738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:102722600-102738600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:102723000-102738200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:102723400-102732200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:102723400-102734000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:102723400-102734200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:102723400-102738600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:102723400-102738600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:102723400-102746400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:102723600-102732400	Strong transcription	Liver	Liver
29	chr7:102723600-102734200	Strong transcription	Placenta	Placenta
30	chr7:102723600-102734600	Strong transcription	Fetal Intestine Large	intestine
31	chr7:102723600-102738600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:102723600-102746400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:102723800-102732600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:102723800-102738600	Strong transcription	Fetal Thymus	thymus
35	chr7:102724000-102732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:102724000-102735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:102724000-102745800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr7:102724000-102760000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:102724000-102770200	Weak transcription	Psoas Muscle	Psoas
40	chr7:102724200-102732400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:102724200-102735800	Strong transcription	Adipose Nuclei	Adipose
42	chr7:102724400-102732000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:102724400-102732400	Strong transcription	Fetal Brain Female	brain
44	chr7:102725200-102770200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:102725400-102753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:102725600-102733800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:102725600-102733800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:102725600-102739400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:102725600-102746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:102725600-102746400	Weak transcription	H9 Cell Line	embryonic stem cell

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