Variant report

Variant	rs3935593
Chromosome Location	chr1:246958265-246958266
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10924827	0.84[JPT][hapmap]
rs10924831	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12042435	0.89[JPT][hapmap]
rs3935608	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6680122	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv525154	chr1:246954166-246963019	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv3340001	chr1:246956154-246958702	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3438105	chr1:246956529-246958527	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246953400-246961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:246955600-246959400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:246956200-246959000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:246956200-246959200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:246956200-246959400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:246956400-246958400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:246956400-246958600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:246956400-246959200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:246956400-246959200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:246956400-246959200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:246956400-246959400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:246956400-246959400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:246956400-246959800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:246956600-246958400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:246956600-246958800	Enhancers	Placenta	Placenta
16	chr1:246956600-246959800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:246956800-246958400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:246956800-246958400	Enhancers	Fetal Stomach	stomach
19	chr1:246956800-246958600	Enhancers	Left Ventricle	heart
20	chr1:246957000-246958400	Enhancers	Gastric	stomach
21	chr1:246957000-246958800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:246957000-246959200	Enhancers	HSMMtube	muscle
23	chr1:246957200-246962400	Weak transcription	Fetal Brain Male	brain
24	chr1:246957400-246958600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:246957400-246959000	Enhancers	Fetal Muscle Leg	muscle
26	chr1:246957600-246958400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:246957600-246958400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:246957600-246958400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:246957600-246958400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:246957600-246958400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:246957600-246958400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:246957600-246958400	Enhancers	Right Atrium	heart
33	chr1:246957600-246958400	Enhancers	NHLF	lung
34	chr1:246957600-246958600	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:246957600-246958600	Enhancers	Esophagus	oesophagus
36	chr1:246957600-246958600	Flanking Active TSS	Hela-S3	cervix
37	chr1:246957600-246958800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:246957600-246958800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:246957600-246958800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:246957600-246958800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr1:246957600-246958800	Enhancers	Lung	lung
42	chr1:246957600-246959000	Enhancers	Right Ventricle	heart
43	chr1:246957600-246959000	Enhancers	HSMM	muscle
44	chr1:246957600-246959400	Enhancers	Fetal Heart	heart
45	chr1:246957800-246958400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:246957800-246958400	Enhancers	Colon Smooth Muscle	Colon
47	chr1:246957800-246958400	Enhancers	NH-A	brain
48	chr1:246957800-246958600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr1:246957800-246958800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:246957800-246959000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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