Variant report

Variant	rs2270707
Chromosome Location	chr1:222837594-222837595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:222837430-222837646	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:222829766-222841488	K562	blood:	n/a	n/a
3	POLR2A	chr1:222837282-222837734	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:222836744-222837997	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:222832045..222836526-chr1:222836686..222840322,4	K562	blood:
2	chr1:222825557..222827908-chr1:222837383..222838889,2	K562	blood:
3	chr1:222817247..222819039-chr1:222835684..222838634,2	MCF-7	breast:
4	chr1:222836221..222837854-chr1:222884380..222886530,2	MCF-7	breast:
5	chr1:222831415..222835034-chr1:222836686..222839635,4	K562	blood:
6	chr1:222837235..222840536-chr1:222884708..222887368,3	MCF-7	breast:
7	chr1:222836136..222838189-chr1:222847780..222849818,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272750	TF binding region
ENSG00000186063	Chromatin interaction
ENSG00000272750	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000162819	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10495198	0.94[ASN][1000 genomes]
rs1133220	0.89[ASN][1000 genomes]
rs11485123	1.00[MEX][hapmap]
rs12043288	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12138316	0.88[ASN][1000 genomes]
rs1391557	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1391558	1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs1498382	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17011666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17011681	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17163313	0.83[ASN][1000 genomes]
rs17163345	0.86[ASN][1000 genomes]
rs17163358	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17163360	0.86[ASN][1000 genomes]
rs17163363	0.86[ASN][1000 genomes]
rs17465637	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17465940	0.96[ASN][1000 genomes]
rs17465982	0.97[ASN][1000 genomes]
rs17532708	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1909195	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1909197	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030076	0.90[MEX][hapmap]
rs2088514	0.92[ASW][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2133187	0.86[ASN][1000 genomes]
rs2133188	0.86[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2133189	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2291832	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2291834	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2378606	0.81[EUR][1000 genomes]
rs28709375	0.93[ASN][1000 genomes]
rs2936020	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2936023	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2936049	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs2936052	0.80[AMR][1000 genomes]
rs2936054	0.80[AMR][1000 genomes]
rs3002146	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3002148	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3008625	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3008629	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008637	0.81[EUR][1000 genomes]
rs34032254	0.86[ASN][1000 genomes]
rs35158675	0.85[ASN][1000 genomes]
rs35175385	0.86[ASN][1000 genomes]
rs35507977	0.95[MEX][hapmap]
rs35626308	0.84[ASN][1000 genomes]
rs35700460	0.86[ASN][1000 genomes]
rs35725247	0.83[ASN][1000 genomes]
rs35806535	1.00[TSI][hapmap]
rs3748626	0.84[ASN][1000 genomes]
rs3811465	1.00[MEX][hapmap]
rs4282830	0.81[ASN][1000 genomes]
rs4575092	0.88[ASN][1000 genomes]
rs4846384	0.82[ASN][1000 genomes]
rs61824331	0.83[ASN][1000 genomes]
rs61827168	0.80[AMR][1000 genomes]
rs6683071	1.00[TSI][hapmap]
rs67180937	0.86[ASN][1000 genomes]
rs71524942	0.83[ASN][1000 genomes]
rs9441835	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9441926	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2270707	HOMER2	trans	parietal	SCAN
rs2270707	C1orf58	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222819000-222841800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:222819200-222841400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:222819200-222841600	Strong transcription	Placenta	Placenta
5	chr1:222819400-222841200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:222820000-222838800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:222820000-222841400	Strong transcription	HSMM	muscle
8	chr1:222820000-222841600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:222820200-222838800	Strong transcription	NHDF-Ad	bronchial
10	chr1:222820200-222841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:222820200-222841400	Strong transcription	NH-A	brain
12	chr1:222820400-222841800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:222820600-222841200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:222820600-222841400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr1:222820800-222841000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:222820800-222841200	Strong transcription	Fetal Intestine Large	intestine
17	chr1:222821000-222840000	Strong transcription	Fetal Kidney	kidney
18	chr1:222821200-222841400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:222821400-222840000	Strong transcription	Fetal Brain Female	brain
20	chr1:222822200-222838800	Strong transcription	Colon Smooth Muscle	Colon
21	chr1:222822200-222841200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:222822200-222841400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:222822400-222841200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:222822400-222841400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:222822600-222840000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:222822600-222841400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:222822600-222841400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:222822800-222840800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:222823000-222838400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:222823000-222839200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:222823000-222841200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:222823000-222841400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:222823200-222840000	Strong transcription	Brain Substantia Nigra	brain
34	chr1:222823200-222840600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:222823200-222841400	Strong transcription	HepG2	liver
36	chr1:222823200-222841400	Strong transcription	K562	blood
37	chr1:222823400-222841400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:222824000-222839600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:222824000-222841400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:222824000-222841400	Strong transcription	A549	lung
41	chr1:222824200-222839800	Strong transcription	Fetal Lung	lung
42	chr1:222825000-222841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:222825200-222839000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:222825600-222840000	Strong transcription	Left Ventricle	heart
45	chr1:222825800-222839600	Strong transcription	Rectal Smooth Muscle	rectum
46	chr1:222826800-222841400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:222827000-222838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:222827000-222845400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:222827200-222839000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:222827400-222837600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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