Variant report

Variant	rs7723689
Chromosome Location	chr5:102895124-102895125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:102878287..102880736-chr5:102894101..102895716,2	MCF-7	breast:
2	chr5:102892137..102895654-chr5:102896197..102900992,7	MCF-7	breast:
3	chr5:102891995..102895213-chr5:102895551..102898444,4	MCF-7	breast:
4	chr5:102891541..102893578-chr5:102893829..102895549,2	K562	blood:
5	chr5:102893524..102895707-chr5:102903466..102905218,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIN1-6	chr5:102895106-102895951	NONHSAT103065

No data

Variant related genes	Relation type
ENSG00000112874	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10057864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061242	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078744	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737902	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157247	1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356231	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406419	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672333	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355522	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797900	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878912	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880267	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71586376	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73190066	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707836	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716935	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7725090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730302	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327885	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1017730	chr5:102887970-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv537834	chr5:102887970-103013575	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1017683	chr5:102887970-103110722	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv537835	chr5:102887970-103110722	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7723689	RAB9BP1	cis	parietal	SCAN
rs7723689	NUDT12	cis	Adipose Subcutaneous	GTEx
rs7723689	NUDT12	Cis_1M	lymphoblastoid	RTeQTL
rs7723689	NUDT12	cis	Esophagus Mucosa	GTEx
rs7723689	NUDT12	cis	Skin Sun Exposed Lower leg	GTEx
rs7723689	NUDT12	cis	lymphoblastoid	seeQTL
rs7723689	ST8SIA4	cis	parietal	SCAN
rs7723689	NUDT12	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102874200-102897400	Weak transcription	Pancreas	Pancrea
2	chr5:102875800-102897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:102879800-102897200	Weak transcription	Brain Germinal Matrix	brain
4	chr5:102879800-102897400	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:102880200-102897200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:102881200-102897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:102882400-102897400	Weak transcription	Psoas Muscle	Psoas
8	chr5:102882800-102897400	Weak transcription	Fetal Heart	heart
9	chr5:102882800-102897600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:102883200-102897400	Weak transcription	GM12878-XiMat	blood
11	chr5:102884600-102897400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:102884600-102897400	Weak transcription	HSMMtube	muscle
13	chr5:102884600-102897400	Weak transcription	NH-A	brain
14	chr5:102884600-102898000	Weak transcription	Small Intestine	intestine
15	chr5:102885200-102897400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:102885200-102897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:102885200-102897400	Weak transcription	Fetal Stomach	stomach
18	chr5:102885200-102897400	Weak transcription	Lung	lung
19	chr5:102885200-102897800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:102885200-102897800	Weak transcription	Esophagus	oesophagus
21	chr5:102885400-102896000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:102885400-102897200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:102885400-102897600	Weak transcription	Colonic Mucosa	Colon
24	chr5:102885400-102897800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:102885400-102897800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:102885600-102897600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:102885800-102897400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:102886200-102897400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:102886200-102897400	Weak transcription	Fetal Brain Female	brain
30	chr5:102886200-102897600	Weak transcription	Primary T cells from cord blood	blood
31	chr5:102886200-102897800	Weak transcription	Placenta	Placenta
32	chr5:102886400-102897200	Weak transcription	Hela-S3	cervix
33	chr5:102886600-102897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:102886600-102897400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:102886600-102897400	Weak transcription	NHLF	lung
36	chr5:102886600-102898000	Weak transcription	Spleen	Spleen
37	chr5:102886800-102896800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:102886800-102897600	Weak transcription	Primary B cells from cord blood	blood
39	chr5:102886800-102897600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr5:102887200-102897000	Weak transcription	Fetal Intestine Small	intestine
41	chr5:102888200-102897000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:102888200-102897000	Weak transcription	Fetal Brain Male	brain
43	chr5:102888200-102897400	Weak transcription	Left Ventricle	heart
44	chr5:102888200-102897400	Weak transcription	Stomach Mucosa	stomach
45	chr5:102888200-102897600	Weak transcription	Aorta	Aorta
46	chr5:102888400-102897400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:102888600-102897800	Weak transcription	Thymus	Thymus
48	chr5:102889600-102897000	Weak transcription	Fetal Kidney	kidney
49	chr5:102889800-102895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:102890000-102896800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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