Variant report

Variant	rs4652130
Chromosome Location	chr1:175809524-175809525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175809125..175809850-chr7:100026224..100026797,2	Hela-S3	cervix:
2	chr1:175809327..175810223-chr10:112260175..112260844,2	Hela-S3	cervix:
3	chr1:175809420..175810333-chr11:63997780..63998448,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNR-5	chr1:175809486-175809542	NONHSAT007760

Variant related genes	Relation type
ENSG00000110011	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10798417	0.92[EUR][1000 genomes]
rs1325913	0.82[EUR][1000 genomes]
rs1325914	0.82[EUR][1000 genomes]
rs1359587	0.84[EUR][1000 genomes]
rs1409143	0.84[EUR][1000 genomes]
rs1522638	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1610270	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1819266	0.81[EUR][1000 genomes]
rs1916052	0.92[EUR][1000 genomes]
rs1925946	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2182310	0.82[EUR][1000 genomes]
rs2182311	0.82[EUR][1000 genomes]
rs34769313	0.82[EUR][1000 genomes]
rs4421556	0.83[EUR][1000 genomes]
rs4462099	0.83[EUR][1000 genomes]
rs4650929	0.84[EUR][1000 genomes]
rs4652119	0.83[EUR][1000 genomes]
rs487948	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs547353	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58209612	0.81[EUR][1000 genomes]
rs59978036	0.82[EUR][1000 genomes]
rs61148850	0.83[EUR][1000 genomes]
rs6425361	0.84[EUR][1000 genomes]
rs6676267	0.84[EUR][1000 genomes]
rs6677856	0.82[EUR][1000 genomes]
rs6699546	0.85[EUR][1000 genomes]
rs7515842	0.84[EUR][1000 genomes]
rs7516044	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7528236	0.86[EUR][1000 genomes]
rs7531762	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7546985	0.84[EUR][1000 genomes]
rs942955	0.84[EUR][1000 genomes]
rs942956	0.84[EUR][1000 genomes]
rs942957	0.84[EUR][1000 genomes]
rs959850	0.87[EUR][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	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv872560	chr1:175648631-175869554	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175804200-175810600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:175806600-175817200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:175808200-175811600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:175808800-175809600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:175808800-175809600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:175808800-175809600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:175808800-175809600	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr1:175808800-175809600	Enhancers	Placenta	Placenta
9	chr1:175808800-175809600	Enhancers	Small Intestine	intestine
10	chr1:175808800-175809600	Flanking Active TSS	HepG2	liver
11	chr1:175808800-175809800	Enhancers	Psoas Muscle	Psoas
12	chr1:175808800-175809800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:175808800-175810000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:175808800-175810200	Flanking Active TSS	Hela-S3	cervix
15	chr1:175808800-175811000	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:175808800-175812000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:175808800-175812000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:175809000-175809600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:175809000-175809600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:175809000-175809600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:175809000-175809600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:175809000-175809600	Enhancers	Lung	lung
23	chr1:175809000-175809800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:175809000-175809800	Enhancers	HMEC	breast
25	chr1:175809000-175810200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:175809000-175810800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr1:175809000-175812000	Enhancers	Fetal Muscle Leg	muscle
28	chr1:175809200-175810000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:175809200-175810800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:175809400-175809600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:175809400-175809600	Bivalent Enhancer	A549	lung
32	chr1:175809400-175809800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:175809400-175811600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:175809400-175811800	Enhancers	Fetal Brain Female	brain
35	chr1:175809400-175811800	Enhancers	Fetal Intestine Small	intestine
36	chr1:175809400-175814800	Enhancers	Fetal Intestine Large	intestine

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