Variant report

Variant	rs2970464
Chromosome Location	chr7:101482413-101482414
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101459242..101461945-chr7:101482180..101485200,3	K562	blood:
2	chr7:101478135..101485394-chr7:101496220..101502463,10	K562	blood:
3	chr7:101456314..101463577-chr7:101474956..101483680,15	K562	blood:
4	chr7:101477818..101480312-chr7:101481428..101485142,3	MCF-7	breast:
5	chr7:101477313..101480622-chr7:101482401..101485267,3	K562	blood:
6	chr7:101481276..101483838-chr7:101497755..101500225,2	K562	blood:
7	chr7:101482049..101483794-chr7:101485598..101488262,2	K562	blood:
8	chr7:101482049..101484240-chr7:101484519..101488262,3	K562	blood:
9	chr7:101481976..101483682-chr7:101490428..101492243,2	MCF-7	breast:
10	chr7:101457482..101461347-chr7:101481909..101485470,5	MCF-7	breast:
11	chr7:101476458..101480622-chr7:101482401..101486770,4	K562	blood:
12	chr7:101468558..101470418-chr7:101481796..101483360,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10270083	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2906717	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906719	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906721	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906741	0.80[AMR][1000 genomes]
rs2906743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906745	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906746	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2906747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906748	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970461	1.00[EUR][1000 genomes]
rs2970462	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970465	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970467	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970469	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970470	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970495	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4236558	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4354243	1.00[JPT][hapmap]
rs73183694	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv521041	chr7:101458144-101496391	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2970464	ACHE	cis	lymphoblastoid	seeQTL
rs2970464	NAPEPLD	cis	parietal	SCAN
rs2970464	ARPC1B	cis	cerebellum	SCAN
rs2970464	SH2B2	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101461200-101486200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:101461800-101489200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:101462200-101484200	Weak transcription	Fetal Kidney	kidney
4	chr7:101463800-101489800	Weak transcription	NHEK	skin
5	chr7:101464600-101488800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:101466800-101489800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:101466800-101498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:101467200-101490400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:101467400-101490400	Weak transcription	Fetal Lung	lung
10	chr7:101468800-101486600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:101469000-101483000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:101469000-101486600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:101469000-101489800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:101469200-101489800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:101469400-101487000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:101469400-101489800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:101469600-101487000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:101469600-101490000	Weak transcription	HepG2	liver
19	chr7:101470000-101496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:101472000-101486800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:101472000-101490400	Weak transcription	Osteobl	bone
22	chr7:101472400-101489400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:101472800-101488600	Weak transcription	Hela-S3	cervix
24	chr7:101473400-101490600	Weak transcription	Primary T cells from cord blood	blood
25	chr7:101474600-101487000	Weak transcription	Dnd41	blood
26	chr7:101474800-101489800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:101475000-101488600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:101475600-101488400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:101475600-101488800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:101475800-101487000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:101476200-101489800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:101476200-101500000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr7:101476400-101487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:101476400-101488200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr7:101476400-101488800	Weak transcription	Esophagus	oesophagus
36	chr7:101476800-101490000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr7:101477800-101487000	Weak transcription	GM12878-XiMat	blood
38	chr7:101478600-101489800	Weak transcription	Fetal Muscle Leg	muscle
39	chr7:101478800-101488600	Weak transcription	Fetal Stomach	stomach
40	chr7:101480400-101488600	Weak transcription	Thymus	Thymus
41	chr7:101481400-101482800	Enhancers	Placenta	Placenta
42	chr7:101481800-101482800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:101481800-101482800	Enhancers	Liver	Liver
44	chr7:101481800-101482800	Enhancers	Left Ventricle	heart
45	chr7:101481800-101482800	Enhancers	Lung	lung
46	chr7:101481800-101482800	Enhancers	Psoas Muscle	Psoas
47	chr7:101481800-101482800	Enhancers	Right Atrium	heart
48	chr7:101482000-101482600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr7:101482000-101482600	Enhancers	A549	lung
50	chr7:101482000-101482800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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