Variant report

Variant	rs3820237
Chromosome Location	chr1:226103363-226103364
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	MXI1	chr1:226102715-226104015	SK-N-SH	brain:	n/a	n/a
2	REST	chr1:226103141-226103582	SK-N-SH	brain:	n/a	chr1:226103258-226103268
3	POLR2A	chr1:226103296-226103459	HepG2	liver:	n/a	n/a
4	REST	chr1:226102623-226103649	H1-neurons	neurons:	n/a	chr1:226103258-226103268
5	GATA2	chr1:226103115-226103613	SH-SY5Y	brain:	n/a	n/a
6	RAD21	chr1:226103075-226103535	SK-N-SH_RA	brain:	n/a	chr1:226103246-226103258
7	POLR2A	chr1:226103313-226112422	K562	blood:	n/a	n/a
8	FOXP2	chr1:226103122-226103480	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226103278..226105384-chr1:226143217..226145668,2	K562	blood:
2	chr1:226085929..226088515-chr1:226102380..226104167,2	MCF-7	breast:
3	chr1:226069654..226072085-chr1:226101693..226103533,2	MCF-7	breast:
4	chr1:226038307..226042475-chr1:226101136..226103388,3	K562	blood:
5	chr1:226086485..226088841-chr1:226103222..226105310,2	K562	blood:

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

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10915902	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10915903	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2295419	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28364597	0.96[ASN][1000 genomes]
rs3753673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3753675	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6661737	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];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	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
2	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
3	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
4	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
5	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
6	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
7	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
9	nsv535314	chr1:226087226-226128261	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226087000-226107200	Weak transcription	Psoas Muscle	Psoas
2	chr1:226087600-226103400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:226087600-226103600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:226087600-226104600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:226096400-226103800	Weak transcription	Gastric	stomach
6	chr1:226097800-226104600	Weak transcription	GM12878-XiMat	blood
7	chr1:226098200-226103600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:226098800-226105200	Weak transcription	K562	blood
9	chr1:226099000-226104800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:226099200-226103600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:226099200-226103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:226099200-226103800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:226099200-226104200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:226099200-226104200	Weak transcription	NHLF	lung
15	chr1:226099200-226104400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:226099200-226105600	Weak transcription	Aorta	Aorta
17	chr1:226099200-226107200	Weak transcription	HUVEC	blood vessel
18	chr1:226099200-226107600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:226099200-226109000	Weak transcription	Colonic Mucosa	Colon
20	chr1:226099400-226104600	Weak transcription	Fetal Kidney	kidney
21	chr1:226099400-226105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:226099400-226106800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:226099400-226107200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:226099400-226107400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:226099400-226109800	Weak transcription	Stomach Mucosa	stomach
26	chr1:226099600-226103400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:226099600-226103400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:226099600-226103600	Weak transcription	Fetal Intestine Large	intestine
29	chr1:226099600-226104200	Weak transcription	Osteobl	bone
30	chr1:226099600-226104400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:226099600-226104400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:226099600-226104600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:226099600-226105000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:226099600-226105200	Weak transcription	A549	lung
35	chr1:226099600-226105800	Weak transcription	HepG2	liver
36	chr1:226099600-226106800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:226099600-226107200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:226099600-226107200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:226099600-226107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:226099600-226107400	Strong transcription	Fetal Stomach	stomach
41	chr1:226099800-226103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:226099800-226103400	Weak transcription	Pancreas	Pancrea
43	chr1:226099800-226103400	Weak transcription	Thymus	Thymus
44	chr1:226099800-226103600	Weak transcription	Fetal Thymus	thymus
45	chr1:226099800-226104200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:226099800-226104400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:226099800-226104400	Weak transcription	Placenta	Placenta
48	chr1:226099800-226104600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:226099800-226104800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:226099800-226105000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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