Variant report

Variant	rs4970956
Chromosome Location	chr1:151516368-151516369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151515840-151516586	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:151516236-151516412	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
2	1:151516085-151535167..1:151592347-151603110	GM12878	blood:
3	chr1:151481542..151488437-chr1:151515636..151525415,14	MCF-7	breast:
4	chr1:151515446..151517713-chr1:151630494..151632395,2	MCF-7	breast:
5	1:151402394-151411623..1:151516085-151535167	GM12878	blood:
6	1:151171193-151178589..1:151516085-151535167	GM12878	blood:

No data

Variant related genes	Relation type
MIR554	TF binding region
ENSG00000143375	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10158855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204842	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034149	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12117155	0.97[EUR][1000 genomes]
rs12753658	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891593	0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2337360	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34589182	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35436273	0.96[EUR][1000 genomes]
rs3828055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56096667	0.97[EUR][1000 genomes]
rs56188938	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521397	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7526319	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549296	1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs868138	0.95[EUR][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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4970956	ZNF687	cis	parietal	SCAN
rs4970956	LINGO4	cis	cerebellum	SCAN
rs4970956	CTSS	cis	cerebellum	SCAN
rs4970956	OTUD7B	cis	cerebellum	SCAN
rs4970956	S100A8	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151513800-151519400	Weak transcription	Left Ventricle	heart
2	chr1:151514000-151519400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151514000-151519400	Weak transcription	HUVEC	blood vessel
4	chr1:151514200-151517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151514200-151519400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:151514200-151519400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:151514200-151519400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151514200-151519600	Weak transcription	Fetal Heart	heart
9	chr1:151514200-151519600	Weak transcription	Ovary	ovary
10	chr1:151514400-151519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:151514400-151519600	Weak transcription	Psoas Muscle	Psoas
12	chr1:151514400-151519800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:151514400-151540800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
15	chr1:151514600-151516400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:151514600-151516400	Enhancers	Pancreas	Pancrea
17	chr1:151514600-151516600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:151514600-151519200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:151514600-151519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:151514600-151519400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:151514600-151519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:151514600-151519600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:151514600-151519800	Weak transcription	Fetal Stomach	stomach
24	chr1:151514800-151519200	Weak transcription	Liver	Liver
25	chr1:151515400-151516600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151515400-151518000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:151515400-151519400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:151515400-151519400	Weak transcription	Small Intestine	intestine
29	chr1:151515400-151519400	Weak transcription	Stomach Mucosa	stomach
30	chr1:151515400-151519600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:151515400-151523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:151515600-151516400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:151515600-151516400	Flanking Active TSS	NHEK	skin
34	chr1:151515600-151516400	Enhancers	NHLF	lung
35	chr1:151515600-151516600	Enhancers	Fetal Intestine Large	intestine
36	chr1:151515600-151517600	Weak transcription	Placenta	Placenta
37	chr1:151515600-151518200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:151515600-151518200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:151515600-151519000	Weak transcription	HepG2	liver
40	chr1:151515600-151519200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:151515600-151519400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:151515600-151519400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:151515600-151519400	Weak transcription	Esophagus	oesophagus
44	chr1:151515600-151519400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:151515600-151519400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:151515600-151519400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:151515600-151519400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:151515600-151519400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:151515600-151519600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:151515600-151519600	Weak transcription	Colonic Mucosa	Colon

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