Variant report

Variant	rs3820238
Chromosome Location	chr1:226078392-226078393
allele	A/C
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	ZBTB7A	chr1:226078231-226078569	HepG2	liver:	n/a	n/a
2	NR2F2	chr1:226078037-226078747	HepG2	liver:	n/a	n/a
3	RXRA	chr1:226078205-226078581	HepG2	liver:	n/a	chr1:226078482-226078495 chr1:226078382-226078401 chr1:226078479-226078499 chr1:226078386-226078400 chr1:226078481-226078495 chr1:226078482-226078495 chr1:226078482-226078495 chr1:226078481-226078497
4	HNF4G	chr1:226078219-226078647	HepG2	liver:	n/a	chr1:226078483-226078496 chr1:226078482-226078495 chr1:226078618-226078630 chr1:226078482-226078495 chr1:226078483-226078495 chr1:226078385-226078400 chr1:226078483-226078495 chr1:226078482-226078497 chr1:226078482-226078496 chr1:226078483-226078495 chr1:226078383-226078401 chr1:226078482-226078495 chr1:226078296-226078318 chr1:226078483-226078495 chr1:226078386-226078398
5	EP300	chr1:226078173-226078632	HepG2	liver:	n/a	n/a
6	CHD2	chr1:226078352-226078406	HepG2	liver:	n/a	n/a
7	FOXA1	chr1:226078346-226078573	HepG2	liver:	n/a	n/a
8	NFIC	chr1:226078276-226078602	HepG2	liver:	n/a	n/a
9	HNF4A	chr1:226078205-226078602	HepG2	liver:	n/a	chr1:226078483-226078496 chr1:226078482-226078495 chr1:226078482-226078495 chr1:226078483-226078495 chr1:226078483-226078495 chr1:226078482-226078497 chr1:226078482-226078496 chr1:226078483-226078495 chr1:226078383-226078401 chr1:226078481-226078496 chr1:226078482-226078495 chr1:226078296-226078318 chr1:226078483-226078495 chr1:226078386-226078398
10	FOXA2	chr1:226078285-226078635	HepG2	liver:	n/a	n/a
11	CTCF	chr1:226078320-226078470	HepG2	liver:	n/a	chr1:226078413-226078422
12	CREB1	chr1:226078119-226079208	HepG2	liver:	n/a	chr1:226078541-226078554
13	ZBTB7A	chr1:226078206-226078561	HepG2	liver:	n/a	n/a
14	JUND	chr1:226078232-226078406	H1-hESC	embryonic stem cell:	n/a	chr1:226078264-226078275
15	NR2F2	chr1:226077982-226079607	HepG2	liver:	n/a	n/a
16	SP1	chr1:226078176-226078690	HepG2	liver:	n/a	chr1:226078228-226078242 chr1:226078343-226078357 chr1:226078346-226078358 chr1:226078347-226078356 chr1:226078346-226078358
17	CEBPD	chr1:226078250-226078612	HepG2	liver:	n/a	n/a
18	RCOR1	chr1:226078365-226078433	HepG2	liver:	n/a	n/a
19	HNF4A	chr1:226078194-226078583	HepG2	liver:	n/a	chr1:226078483-226078496 chr1:226078482-226078495 chr1:226078482-226078495 chr1:226078483-226078495 chr1:226078483-226078495 chr1:226078482-226078497 chr1:226078482-226078496 chr1:226078483-226078495 chr1:226078383-226078401 chr1:226078481-226078496 chr1:226078482-226078495 chr1:226078296-226078318 chr1:226078483-226078495 chr1:226078386-226078398
20	FOSL2	chr1:226078105-226078600	HepG2	liver:	n/a	chr1:226078543-226078552 chr1:226078264-226078275
21	FOXA1	chr1:226078177-226078683	HepG2	liver:	n/a	n/a
22	HDAC2	chr1:226078234-226078629	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
2	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:

Variant related genes	Relation type
LEFTY1	TF binding region
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1877726	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653437	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226078600	Weak transcription	Lung	lung
2	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:226071800-226078800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:226072000-226081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:226072000-226081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:226072000-226082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:226073200-226079800	Enhancers	Liver	Liver
8	chr1:226074800-226078800	Enhancers	Fetal Stomach	stomach
9	chr1:226075400-226079200	Enhancers	Ovary	ovary
10	chr1:226075800-226079000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:226076200-226078800	Enhancers	A549	lung
12	chr1:226076200-226079000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:226076400-226079000	Enhancers	Placenta	Placenta
14	chr1:226076600-226078600	Enhancers	Fetal Muscle Leg	muscle
15	chr1:226076600-226079000	Enhancers	Fetal Intestine Small	intestine
16	chr1:226076600-226079800	Enhancers	Stomach Mucosa	stomach
17	chr1:226076600-226080400	Enhancers	Pancreas	Pancrea
18	chr1:226076800-226078600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:226076800-226079000	Enhancers	Fetal Lung	lung
20	chr1:226076800-226079600	Enhancers	Fetal Intestine Large	intestine
21	chr1:226076800-226079800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:226076800-226079800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:226076800-226079800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:226076800-226084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:226077000-226078400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:226077000-226079200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr1:226077000-226085200	Weak transcription	Spleen	Spleen
28	chr1:226077000-226099000	Weak transcription	Right Atrium	heart
29	chr1:226077200-226078800	Weak transcription	K562	blood
30	chr1:226077200-226079000	Enhancers	Colonic Mucosa	Colon
31	chr1:226077200-226079200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:226077400-226078400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:226077400-226079200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:226077400-226079600	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:226077400-226079800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:226077400-226079800	Flanking Active TSS	HepG2	liver
37	chr1:226077400-226084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:226077600-226079200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:226077600-226079400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr1:226077800-226078400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:226077800-226078600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:226077800-226079200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:226077800-226079800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr1:226078000-226078400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr1:226078000-226078400	Enhancers	Osteobl	bone
46	chr1:226078000-226078600	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:226078000-226079000	Weak transcription	Fetal Kidney	kidney
48	chr1:226078000-226080400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:226078200-226078400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:226078200-226078600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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