Variant report

Variant	rs1863910
Chromosome Location	chr3:134092058-134092059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
2	SP4	chr3:134092016-134092681	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF7	chr3:134091817-134093873	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr3:134091790-134094514	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134091915-134091931 chr3:134092363-134092379 chr3:134092748-134092757
5	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
6	RCOR1	chr3:134091947-134094409	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:134091825-134094472	Hela-S3	cervix:	n/a	n/a
8	RFX5	chr3:134091836-134094520	Hela-S3	cervix:	n/a	n/a
9	SP1	chr3:134092003-134092800	A549	lung:	n/a	n/a
10	FOXP2	chr3:134091985-134092262	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr3:134091789-134093988	HUVEC	blood vessel:	n/a	n/a
12	SIN3AK20	chr3:134091772-134092923	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr3:134091947-134094381	ECC-1	luminal epithelium:	n/a	n/a
14	MAZ	chr3:134092048-134093871	HepG2	liver:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
15	TCF12	chr3:134091783-134094382	ECC-1	luminal epithelium:	n/a	chr3:134092197-134092205 chr3:134093938-134093947 chr3:134091915-134091925
16	MXI1	chr3:134092032-134092827	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:134090064-134093861	SK-N-SH	brain:	n/a	n/a
18	USF2	chr3:134091903-134092715	H1-hESC	embryonic stem cell:	n/a	n/a
19	GATA2	chr3:134091958-134092513	SH-SY5Y	brain:	n/a	chr3:134092098-134092107
20	REST	chr3:134092022-134092322	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr3:134092007-134092839	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:134090674-134093906	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:134079921-134092871	ECC-1	luminal epithelium:	n/a	n/a
24	RFX5	chr3:134092055-134092229	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr3:134091772-134094474	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr3:134091977-134092302	H1-hESC	embryonic stem cell:	n/a	chr3:134092197-134092205
27	SMC3	chr3:134091260-134094465	Hela-S3	cervix:	n/a	n/a
28	ATF2	chr3:134091851-134093550	H1-hESC	embryonic stem cell:	n/a	chr3:134092660-134092671 chr3:134092658-134092672
29	JUND	chr3:134091923-134094010	H1-hESC	embryonic stem cell:	n/a	chr3:134092661-134092670
30	JUND	chr3:134091985-134092900	SK-N-SH	brain:	n/a	chr3:134092661-134092670
31	TEAD4	chr3:134091954-134094075	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:134091780-134094364	PANC-1	pancreas:	n/a	n/a
33	NRF1	chr3:134091989-134092165	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:134091951-134094281	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:134091456-134094015	H1-neurons	neurons:	n/a	n/a
36	BRCA1	chr3:134092026-134092753	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
38	SIN3A	chr3:134091883-134094577	H1-hESC	embryonic stem cell:	n/a	chr3:134093487-134093500 chr3:134093529-134093542
39	MAX	chr3:134091975-134092867	MCF-7	breast:	n/a	chr3:134092343-134092353
40	TFAP2C	chr3:134092025-134094581	Hela-S3	cervix:	n/a	chr3:134092572-134092587 chr3:134093979-134093988 chr3:134092550-134092565 chr3:134093841-134093856
41	POLR2A	chr3:134089460-134093902	ProgFib	skin:	n/a	n/a
42	POLR2A	chr3:134088558-134094000	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr3:134091984-134094458	H1-hESC	embryonic stem cell:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
44	TAF1	chr3:134091818-134092807	H1-neurons	neurons:	n/a	n/a
45	TAF1	chr3:134092000-134094372	ECC-1	luminal epithelium:	n/a	n/a
46	TEAD4	chr3:134091666-134094419	ECC-1	luminal epithelium:	n/a	chr3:134091797-134091806
47	SIN3AK20	chr3:134092000-134094195	MCF-7	breast:	n/a	n/a
48	POLR2A	chr3:134091820-134094033	H1-neurons	neurons:	n/a	n/a
49	GATA3	chr3:134091971-134094399	A549	lung:	n/a	chr3:134092098-134092107
50	REST	chr3:134090845-134094305	H1-neurons	neurons:	n/a	chr3:134091280-134091300 chr3:134093018-134093031 chr3:134093487-134093500 chr3:134092989-134093002 chr3:134091286-134091300 chr3:134093839-134093848

No.	Distal block	Cell Line	Cell type
1	chr3:134091805..134100491-chr3:134198620..134206897,15	MCF-7	breast:
2	chr3:134089711..134094738-chr3:134202793..134208651,12	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr13:73301301..73302072-chr3:134091793..134092639,2	Hela-S3	cervix:

Variant related genes	Relation type
AMOTL2	TF binding region
ENSG00000136122	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000240006	Chromatin interaction
ENSG00000204899	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10755085	0.96[ASN][1000 genomes]
rs10755086	0.96[ASN][1000 genomes]
rs11708815	0.85[ASN][1000 genomes]
rs11719057	0.85[ASN][1000 genomes]
rs12495847	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496438	0.96[ASN][1000 genomes]
rs13075185	0.85[ASN][1000 genomes]
rs13322269	1.00[ASN][1000 genomes]
rs1353776	0.80[ASN][1000 genomes]
rs1353777	1.00[ASN][1000 genomes]
rs1353778	0.96[ASN][1000 genomes]
rs1466827	0.89[ASN][1000 genomes]
rs3732852	0.80[ASN][1000 genomes]
rs3755762	0.96[ASN][1000 genomes]
rs3773820	0.85[ASN][1000 genomes]
rs3821705	0.80[ASN][1000 genomes]
rs4264700	0.80[ASN][1000 genomes]
rs4974489	0.80[ASN][1000 genomes]
rs4974491	0.80[ASN][1000 genomes]
rs4974498	0.80[ASN][1000 genomes]
rs6439478	0.80[ASN][1000 genomes]
rs6786148	0.80[ASN][1000 genomes]
rs7613066	0.85[ASN][1000 genomes]
rs9817900	0.80[ASN][1000 genomes]
rs9853621	0.80[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:134087200-134092600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:134087600-134092400	Transcr. at gene 5' and 3'	A549	lung
4	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr3:134088200-134092600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:134088400-134092200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:134088400-134092600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:134088600-134092400	Transcr. at gene 5' and 3'	NHLF	lung
10	chr3:134089200-134092600	Transcr. at gene 5' and 3'	NHEK	skin
11	chr3:134089400-134092400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
12	chr3:134089800-134092200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
13	chr3:134090400-134094400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr3:134090600-134092600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
15	chr3:134090600-134093600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:134091000-134092400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:134091000-134094000	Active TSS	Fetal Kidney	kidney
18	chr3:134091200-134092200	Flanking Active TSS	Fetal Lung	lung
19	chr3:134091200-134092400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:134091200-134093600	Active TSS	Esophagus	oesophagus
21	chr3:134091200-134093600	Active TSS	HSMMtube	muscle
22	chr3:134091200-134093800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:134091200-134093800	Active TSS	Aorta	Aorta
24	chr3:134091200-134094000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:134091200-134094000	Active TSS	Lung	lung
26	chr3:134091400-134092200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr3:134091400-134092600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:134091400-134092600	Flanking Active TSS	Liver	Liver
29	chr3:134091400-134092800	Active TSS	Spleen	Spleen
30	chr3:134091400-134093400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:134091400-134093600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:134091400-134093600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:134091400-134093600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:134091400-134093600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr3:134091400-134093800	Active TSS	Placenta Amnion	Placenta Amnion
36	chr3:134091400-134094000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr3:134091400-134094000	Active TSS	Colon Smooth Muscle	Colon
38	chr3:134091400-134094000	Active TSS	NHDF-Ad	bronchial
39	chr3:134091400-134094200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:134091400-134094400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:134091600-134092200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:134091600-134092200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr3:134091600-134092400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:134091600-134093000	Active TSS	Duodenum Mucosa	Duodenum
45	chr3:134091600-134093400	Active TSS	HMEC	breast
46	chr3:134091600-134093600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:134091600-134093600	Active TSS	Adipose Nuclei	Adipose
48	chr3:134091600-134093600	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:134091600-134093600	Active TSS	Brain Hippocampus Middle	brain
50	chr3:134091600-134093600	Active TSS	Brain Inferior Temporal Lobe	brain

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