Variant report

Variant	rs17043167
Chromosome Location	chr2:113276899-113276900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113275893..113278850-chr2:113299428..113303764,5	K562	blood:
2	chr2:112641308..112643198-chr2:113276179..113278501,2	MCF-7	breast:
3	chr2:113275838..113278261-chr2:113340467..113342078,2	K562	blood:

Variant related genes	Relation type
ENSG00000153107	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10153558	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10153801	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11123137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1127264	0.96[ASN][1000 genomes]
rs11644	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs11899598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465241	0.96[ASN][1000 genomes]
rs12465446	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030618	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437673	0.88[CEU][hapmap]
rs1437675	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[TSI][hapmap]
rs1545133	0.88[CEU][hapmap]
rs17043158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542310	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082454	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35419160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3910512	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849073	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs4849074	0.88[CEU][hapmap]
rs56010201	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62157527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542059	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542060	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6718241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718489	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs6760014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569407	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580213	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers 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 target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs17043167	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs17043167	TTL	cis	Skin Sun Exposed Lower leg	GTEx
rs17043167	RGPD8	cis	Muscle Skeletal	GTEx
rs17043167	POLR1B	cis	cerebellum	SCAN
rs17043167	POLR1B	cis	parietal	SCAN
rs17043167	IL1F8	cis	parietal	SCAN
rs17043167	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs17043167	RGPD8	cis	Nerve Tibial	GTEx
rs17043167	RGPD8	cis	Artery Tibial	GTEx
rs17043167	FBLN7	cis	parietal	SCAN
rs17043167	RGPD8	cis	lung	GTEx
rs17043167	LOC653596	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241000-113277200	Weak transcription	Gastric	stomach
2	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
3	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
4	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
9	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
12	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
13	chr2:113252000-113277800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:113252200-113277800	Weak transcription	Psoas Muscle	Psoas
15	chr2:113252800-113277200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:113253000-113277000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:113253000-113277000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:113253000-113277800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:113253200-113277000	Weak transcription	Lung	lung
20	chr2:113253200-113277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:113253400-113277800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:113253800-113277800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:113260000-113277000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:113260000-113277800	Weak transcription	Aorta	Aorta
25	chr2:113260200-113277200	Weak transcription	Thymus	Thymus
26	chr2:113260600-113277800	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:113260600-113278000	Weak transcription	Ovary	ovary
28	chr2:113260800-113277000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:113260800-113277200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:113260800-113277200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:113260800-113277200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:113260800-113277200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:113260800-113277200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:113260800-113277200	Weak transcription	Placenta	Placenta
35	chr2:113260800-113277200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:113260800-113277200	Weak transcription	NHLF	lung
37	chr2:113260800-113277600	Weak transcription	Brain Angular Gyrus	brain
38	chr2:113260800-113277800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:113260800-113277800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:113260800-113277800	Weak transcription	NHEK	skin
41	chr2:113260800-113279400	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:113260800-113286200	Weak transcription	Fetal Brain Male	brain
43	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
44	chr2:113267000-113277200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:113267400-113277200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:113267400-113290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr2:113267600-113277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:113268000-113277800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:113268000-113286400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:113269000-113277400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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