Variant report

Variant	rs8071003
Chromosome Location	chr17:46009888-46009889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45974031..45975859-chr17:46008200..46010414,2	MCF-7	breast:
2	chr17:46003485..46006244-chr17:46007523..46010248,2	K562	blood:
3	chr17:45973395..45975502-chr17:46008931..46011121,2	MCF-7	breast:
4	chr17:46007857..46010307-chr17:46016278..46019958,3	K562	blood:
5	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108439	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000234494	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.86[ASN][1000 genomes]
rs1130932	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652827	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655068	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.85[ASN][1000 genomes]
rs12939739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228251	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.85[ASN][1000 genomes]
rs34593510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	0.85[ASN][1000 genomes]
rs4793737	0.85[ASN][1000 genomes]
rs4794261	0.86[ASN][1000 genomes]
rs4794286	0.89[ASN][1000 genomes]
rs4794332	0.85[ASN][1000 genomes]
rs6503934	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.86[ASN][1000 genomes]
rs72840237	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8071003	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs8071003	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
2	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
3	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
4	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
5	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:45999000-46010400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr17:45999600-46010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:46001000-46010600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:46002400-46013400	Weak transcription	Stomach Mucosa	stomach
12	chr17:46003000-46012200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:46003200-46012000	Weak transcription	HMEC	breast
14	chr17:46003200-46012000	Weak transcription	NHDF-Ad	bronchial
15	chr17:46003200-46012200	Weak transcription	NH-A	brain
16	chr17:46003200-46012200	Weak transcription	NHEK	skin
17	chr17:46003200-46014200	Weak transcription	GM12878-XiMat	blood
18	chr17:46003200-46018400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:46004400-46012600	Weak transcription	Hela-S3	cervix
20	chr17:46004600-46013200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:46004600-46018200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:46005400-46012400	Weak transcription	NHLF	lung
23	chr17:46005400-46017400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:46005400-46018200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr17:46006200-46017800	Weak transcription	Small Intestine	intestine
26	chr17:46006600-46011200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:46006600-46013400	Weak transcription	Right Atrium	heart
28	chr17:46006800-46011000	Strong transcription	Fetal Stomach	stomach
29	chr17:46006800-46015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:46007000-46010400	Weak transcription	A549	lung
31	chr17:46007000-46011200	Strong transcription	Fetal Intestine Small	intestine
32	chr17:46007000-46012000	Weak transcription	HSMM	muscle
33	chr17:46007000-46012200	Weak transcription	Osteobl	bone
34	chr17:46007000-46015600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:46007000-46018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:46007000-46018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:46007200-46018200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:46007600-46012200	Weak transcription	HSMMtube	muscle
39	chr17:46007600-46013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:46007600-46017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:46007600-46018200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr17:46007600-46018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:46007800-46010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:46007800-46018200	Weak transcription	Colonic Mucosa	Colon
45	chr17:46007800-46018400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr17:46007800-46018800	Weak transcription	Gastric	stomach
47	chr17:46008000-46010400	Weak transcription	Thymus	Thymus
48	chr17:46008000-46012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:46008000-46013200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr17:46008000-46013200	Weak transcription	Placenta Amnion	Placenta Amnion

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