Variant report

Variant	rs1870939
Chromosome Location	chr1:155055496-155055497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr1:155051293-155055708	NT2-D1	testis:	n/a	n/a
2	MAX	chr1:155055083-155055521	ECC-1	luminal epithelium:	n/a	chr1:155055262-155055271
3	GABPA	chr1:155055400-155056116	MCF-7	breast:	n/a	n/a
4	STAT1	chr1:155055462-155055595	GM12878	blood:	n/a	n/a
5	FOXA1	chr1:155055259-155055605	T-47D	breast:	n/a	n/a
6	MAX	chr1:155055118-155056138	MCF-7	breast:	n/a	chr1:155055262-155055271 chr1:155055977-155055986
7	ELF1	chr1:155055333-155056151	MCF-7	breast:	n/a	n/a
8	NR2F2	chr1:155055351-155056272	MCF-7	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154970467..154977420-chr1:155052491..155060843,19	MCF-7	breast:
2	chr1:155054721..155059011-chr1:155196588..155199418,3	K562	blood:
3	chr1:154941567..154943092-chr1:155053762..155055661,2	MCF-7	breast:
4	chr1:154967268..154977621-chr1:155049775..155059069,28	MCF-7	breast:
5	chr1:155034804..155037518-chr1:155055135..155058799,58	K562	blood:
6	chr1:154528624..154530149-chr1:155054658..155056691,2	MCF-7	breast:
7	chr1:154989227..154992640-chr1:155054340..155057432,4	MCF-7	breast:
8	chr1:154933652..154935727-chr1:155055132..155058797,5	MCF-7	breast:
9	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
10	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
11	chr1:155052471..155058946-chr1:155106509..155113930,10	K562	blood:
12	chr1:155020796..155024695-chr1:155055166..155059924,7	K562	blood:
13	chr1:155055391..155058180-chr1:155162719..155165085,4	K562	blood:
14	chr1:155052798..155059451-chr1:155162483..155166744,9	K562	blood:
15	chr1:154925003..154929054-chr1:155054895..155057237,4	K562	blood:
16	chr1:155052864..155055747-chr1:155138816..155141443,2	K562	blood:
17	chr1:154971672..154974810-chr1:155055018..155057601,4	K562	blood:

No data

Variant related genes	Relation type
EFNA3	TF binding region
ENSG00000185499	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000202027	Chromatin interaction
ENSG00000163348	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10796939	0.90[ASN][1000 genomes]
rs10908454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908456	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264312	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264313	0.97[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264318	0.81[AMR][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264321	1.00[ASN][1000 genomes]
rs11264322	0.97[ASN][1000 genomes]
rs11264327	0.93[ASN][1000 genomes]
rs11264328	0.93[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11581730	0.81[AMR][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.97[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	1.00[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12145362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306124	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.95[ASN][1000 genomes]
rs4361977	1.00[ASN][1000 genomes]
rs4625273	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	1.00[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7366138	0.95[ASN][1000 genomes]
rs7366355	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7367207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7367758	0.97[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7534162	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.88[ASN][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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155050800-155055800	Enhancers	Lung	lung
2	chr1:155050800-155056000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:155051000-155055600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:155052000-155055800	Bivalent Enhancer	GM12878-XiMat	blood
5	chr1:155052400-155055600	Bivalent Enhancer	Left Ventricle	heart
6	chr1:155052600-155055600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
7	chr1:155053200-155057200	Bivalent Enhancer	Fetal Thymus	thymus
8	chr1:155053600-155055600	Bivalent Enhancer	Fetal Heart	heart
9	chr1:155053600-155057000	Enhancers	Pancreas	Pancrea
10	chr1:155053600-155057200	Bivalent Enhancer	Placenta	Placenta
11	chr1:155053600-155057200	Enhancers	Gastric	stomach
12	chr1:155053800-155055800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:155053800-155057000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr1:155054000-155055600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
15	chr1:155054200-155055600	Bivalent Enhancer	Small Intestine	intestine
16	chr1:155054200-155055600	Weak transcription	Hela-S3	cervix
17	chr1:155054400-155055600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:155054400-155055800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr1:155054400-155056200	Bivalent Enhancer	Fetal Brain Male	brain
20	chr1:155054400-155057000	Bivalent Enhancer	Fetal Lung	lung
21	chr1:155054400-155057200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:155054400-155057200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:155054400-155057200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:155054600-155055600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr1:155054600-155055600	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr1:155054600-155055800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:155054600-155056200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
28	chr1:155054600-155056200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
29	chr1:155054600-155057200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:155054800-155055600	Bivalent Enhancer	Brain Substantia Nigra	brain
31	chr1:155054800-155055600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
32	chr1:155054800-155055800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:155054800-155055800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
34	chr1:155054800-155056000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
35	chr1:155054800-155056800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr1:155054800-155057200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr1:155055000-155055600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr1:155055000-155055600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr1:155055000-155056000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
40	chr1:155055000-155056800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:155055000-155057000	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr1:155055000-155057000	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr1:155055200-155055600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:155055200-155055600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:155055200-155055600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
46	chr1:155055200-155055600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr1:155055200-155055600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
48	chr1:155055200-155055600	Bivalent Enhancer	Liver	Liver
49	chr1:155055200-155055600	Bivalent Enhancer	Brain Germinal Matrix	brain
50	chr1:155055200-155055600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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