Variant report

Variant	rs10198001
Chromosome Location	chr2:85743357-85743358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85739058..85741304-chr2:85742843..85744856,2	K562	blood:
2	chr2:85739186..85748448-chr2:85762345..85768928,20	MCF-7	breast:
3	chr2:85741540..85743418-chr2:85749217..85750940,2	MCF-7	breast:
4	chr2:85741968..85744955-chr2:85763802..85767184,3	K562	blood:
5	chr2:85742777..85745374-chr2:85747062..85748764,2	MCF-7	breast:
6	chr2:85739581..85746336-chr2:85762702..85767789,18	MCF-7	breast:
7	chr2:85647942..85651306-chr2:85740922..85744191,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152292	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10166612	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10167018	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10172793	0.87[ASN][1000 genomes]
rs10174551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10179904	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10187218	0.80[ASN][1000 genomes]
rs10190585	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10196357	0.87[ASN][1000 genomes]
rs10198761	0.80[ASN][1000 genomes]
rs10202828	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10496316	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12714142	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12714143	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714144	0.87[ASN][1000 genomes]
rs12714147	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12994163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs13000511	0.80[ASN][1000 genomes]
rs13387999	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13394092	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13406611	0.87[ASN][1000 genomes]
rs13406935	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13408713	0.87[ASN][1000 genomes]
rs13409377	0.80[ASN][1000 genomes]
rs13421434	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13422558	0.87[ASN][1000 genomes]
rs13425821	0.80[ASN][1000 genomes]
rs13426038	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13429968	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13431159	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13431962	0.87[ASN][1000 genomes]
rs13432584	0.80[ASN][1000 genomes]
rs17430670	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17508727	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17735885	0.87[ASN][1000 genomes]
rs2121397	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs28398892	0.87[ASN][1000 genomes]
rs28479378	0.84[ASN][1000 genomes]
rs28800839	0.87[ASN][1000 genomes]
rs28810460	0.87[ASN][1000 genomes]
rs34212016	0.80[ASN][1000 genomes]
rs34214220	0.80[ASN][1000 genomes]
rs34669893	0.87[ASN][1000 genomes]
rs34824628	0.87[ASN][1000 genomes]
rs56359002	0.80[ASN][1000 genomes]
rs62165899	0.87[ASN][1000 genomes]
rs6727614	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10198001	POLR1A,LOC90784	cis	thalamus	BrainEAC
rs10198001	GGCX	cis	Nerve Tibial	GTEx
rs10198001	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85732400-85743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:85732400-85744200	Weak transcription	Gastric	stomach
3	chr2:85733200-85743800	Weak transcription	Esophagus	oesophagus
4	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:85734800-85743600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:85738800-85743400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:85738800-85744200	Weak transcription	Small Intestine	intestine
10	chr2:85739000-85743400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:85739000-85743400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:85739000-85743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:85739000-85743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:85739000-85743600	Weak transcription	HUVEC	blood vessel
15	chr2:85739000-85743800	Weak transcription	Placenta	Placenta
16	chr2:85739200-85743400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:85741000-85743600	Weak transcription	Colonic Mucosa	Colon
18	chr2:85741200-85743400	Enhancers	A549	lung
19	chr2:85742000-85743800	Enhancers	Hela-S3	cervix
20	chr2:85742200-85743800	Enhancers	HepG2	liver
21	chr2:85742200-85744600	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:85742200-85744600	Enhancers	Fetal Intestine Small	intestine
23	chr2:85742200-85744600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:85742400-85744800	Weak transcription	Psoas Muscle	Psoas
25	chr2:85742600-85743400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr2:85742600-85745200	Enhancers	Fetal Intestine Large	intestine
27	chr2:85742800-85744200	Weak transcription	Pancreas	Pancrea
28	chr2:85742800-85745200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr2:85743200-85744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:85743200-85745600	Enhancers	Stomach Mucosa	stomach

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