Variant report

Variant	rs202018
Chromosome Location	chr6:13301502-13301503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13298717..13301545-chr6:13301638..13304448,3	K562	blood:
2	chr6:13282855..13286239-chr6:13300914..13304700,4	K562	blood:
3	chr6:13274083..13277421-chr6:13297082..13301885,5	K562	blood:
4	chr6:13293047..13295982-chr6:13300305..13302039,2	K562	blood:
5	chr6:13299774..13302593-chr6:13305903..13308627,2	K562	blood:
6	chr6:13274184..13276021-chr6:13298954..13301885,2	K562	blood:

Variant related genes	Relation type
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1223397	0.81[JPT][hapmap]
rs13203254	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs202016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202022	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20499	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs20500	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439535	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439540	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439543	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439544	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458300	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458309	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458314	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496149	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496151	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496152	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496153	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496154	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496157	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919685	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919686	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001966	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001967	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001968	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364493	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3817737	0.80[ASN][1000 genomes]
rs3817738	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817741	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817742	0.80[ASN][1000 genomes]
rs402705	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453877	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59639740	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617580	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs641758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349564	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381884	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9395602	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs957175	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957176	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202018	RP1-257A7.4	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
5	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
7	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
8	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
10	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:13290200-13302800	Weak transcription	NHEK	skin
12	chr6:13290400-13310400	Strong transcription	Dnd41	blood
13	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
14	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
15	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
16	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:13291600-13302400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:13291600-13302400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:13291600-13302600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:13291600-13302600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:13291600-13305800	Strong transcription	Thymus	Thymus
23	chr6:13291800-13301800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:13292000-13302600	Strong transcription	Fetal Intestine Large	intestine
26	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:13292400-13302600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:13293000-13302800	Strong transcription	Fetal Lung	lung
30	chr6:13293200-13305400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:13294200-13302600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:13295000-13304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:13295200-13302200	Weak transcription	NHDF-Ad	bronchial
34	chr6:13295200-13305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:13295400-13302000	Weak transcription	Fetal Brain Male	brain
36	chr6:13295400-13302600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:13295600-13302600	Weak transcription	Esophagus	oesophagus
38	chr6:13295600-13302800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:13295800-13301600	Weak transcription	Brain Anterior Caudate	brain
40	chr6:13295800-13302400	Weak transcription	A549	lung
41	chr6:13295800-13302600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:13295800-13302600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:13295800-13302800	Weak transcription	HMEC	breast
44	chr6:13295800-13303000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:13296200-13302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:13296200-13302600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:13296200-13302600	Weak transcription	Colonic Mucosa	Colon
48	chr6:13296600-13302600	Weak transcription	Pancreas	Pancrea
49	chr6:13297000-13302600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:13297200-13302400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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