Variant report

Variant	rs2562730
Chromosome Location	chr7:128100038-128100039
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:128094251..128097600-chr7:128097947..128102494,8	K562	blood:
2	chr7:128066135..128077193-chr7:128094256..128102719,54	MCF-7	breast:
3	chr7:128046088..128049904-chr7:128098273..128102609,4	K562	blood:
4	chr7:128082541..128090035-chr7:128090151..128101015,22	MCF-7	breast:
5	chr7:128065568..128066529-chr7:128099108..128100221,4	K562	blood:
6	chr7:128069994..128071005-chr7:128099002..128100606,7	MCF-7	breast:
7	chr7:128048057..128050618-chr7:128098751..128100517,2	MCF-7	breast:
8	chr7:128098205..128100109-chr7:128100150..128103100,2	MCF-7	breast:
9	chr7:128065135..128067914-chr7:128098635..128100685,2	K562	blood:
10	chr7:128070428..128073149-chr7:128099474..128101225,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238590	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000228700	Chromatin interaction
ENSG00000135245	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10229016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10229394	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10230632	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10230965	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10245559	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10251597	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10271590	0.85[ASN][1000 genomes]
rs1035971	0.89[TSI][hapmap]
rs1065267	0.84[CEU][hapmap]
rs11770116	1.00[CHB][hapmap]
rs11980741	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12672625	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs13245629	1.00[JPT][hapmap]
rs1560214	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288548	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2288549	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2402892	0.85[TSI][hapmap]
rs2402895	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562731	0.80[ASN][1000 genomes]
rs2562732	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562733	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2562734	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562740	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2732394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732397	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2732432	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28479078	0.85[ASN][1000 genomes]
rs3097361	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35586323	0.84[ASN][1000 genomes]
rs3958071	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4728108	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731446	0.85[AMR][1000 genomes]
rs4731448	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4731450	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731453	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731454	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731455	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5009156	0.85[ASN][1000 genomes]
rs58979384	0.85[ASN][1000 genomes]
rs6467178	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947697	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6948333	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6959839	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7797240	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv608401	chr7:128083454-128108776	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2562730	ZNF800	cis	parietal	SCAN
rs2562730	IL31RA	trans	parietal	SCAN
rs2562730	FAM71F2	cis	cerebellum	SCAN
rs2562730	TMEM209	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128096400-128116400	Weak transcription	Lung	lung
2	chr7:128096800-128101400	Weak transcription	HSMMtube	muscle
3	chr7:128097200-128100200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:128097400-128103400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128097400-128107800	Weak transcription	Spleen	Spleen
6	chr7:128097600-128101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:128097600-128102800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:128097600-128116200	Weak transcription	Fetal Kidney	kidney
9	chr7:128097600-128116200	Weak transcription	Left Ventricle	heart
10	chr7:128097800-128102000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:128097800-128116400	Weak transcription	Fetal Stomach	stomach
12	chr7:128097800-128116400	Weak transcription	Gastric	stomach
13	chr7:128097800-128116400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:128098200-128102800	Weak transcription	Right Ventricle	heart
15	chr7:128098200-128116400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:128098200-128116400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:128098400-128100200	Enhancers	Fetal Lung	lung
18	chr7:128098400-128101600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:128098400-128108000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:128098600-128100200	Genic enhancers	Brain Germinal Matrix	brain
21	chr7:128098600-128102000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:128098600-128102600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:128098600-128104800	Weak transcription	Osteobl	bone
24	chr7:128098600-128116200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:128098800-128108200	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:128099000-128100200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr7:128099000-128100200	Flanking Active TSS	GM12878-XiMat	blood
28	chr7:128099000-128102600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:128099000-128116200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:128099000-128116400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:128099200-128100200	Enhancers	Dnd41	blood
32	chr7:128099200-128100400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr7:128099200-128102400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:128099200-128116400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:128099400-128100200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:128099400-128100600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr7:128099400-128116200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:128099400-128116400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr7:128099600-128100200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr7:128099800-128100200	Active TSS	Brain Anterior Caudate	brain
41	chr7:128099800-128100200	Enhancers	K562	blood
42	chr7:128099800-128100600	Weak transcription	NHDF-Ad	bronchial
43	chr7:128099800-128102200	Weak transcription	Fetal Heart	heart
44	chr7:128099800-128102600	Weak transcription	NHLF	lung
45	chr7:128099800-128102800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:128099800-128102800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr7:128099800-128103200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:128099800-128104800	Weak transcription	Brain Substantia Nigra	brain
49	chr7:128099800-128116200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:128099800-128116200	Weak transcription	Duodenum Mucosa	Duodenum

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