Variant report

Variant	rs6930790
Chromosome Location	chr6:86219559-86219560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86219269-86219649	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:86219291-86219598	K562	blood:	n/a	n/a
3	POLR2A	chr6:86218621-86220207	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86215713..86217410-chr6:86218817..86221712,2	K562	blood:
2	chr6:86212509..86214733-chr6:86218733..86220237,2	K562	blood:

Variant related genes	Relation type
SNX14	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12055597	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12524836	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs12528808	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12664908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1570311	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1590279	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2229524	0.93[ASN][1000 genomes]
rs3812137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144166	0.81[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4327657	0.93[ASN][1000 genomes]
rs4373339	0.92[ASW][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs4400191	0.92[ASW][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs4458647	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4487548	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4565270	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6902638	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6902904	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6910543	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6913634	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6923017	0.87[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs73751215	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7744309	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs7745560	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7746186	0.81[ASN][1000 genomes]
rs7749600	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7752105	1.00[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7771187	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7771366	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7775788	0.87[ASN][1000 genomes]
rs9344527	0.81[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9344529	0.81[ASN][1000 genomes]
rs9344530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344538	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9351063	1.00[ASN][1000 genomes]
rs9353319	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs9353321	1.00[ASN][1000 genomes]
rs9353323	0.87[ASN][1000 genomes]
rs9353324	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs9359656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9362223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362224	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9362225	0.93[ASN][1000 genomes]
rs9362226	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9444353	1.00[ASN][1000 genomes]
rs9444356	0.81[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9450286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450289	1.00[ASN][1000 genomes]
rs9450294	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs9450295	1.00[ASN][1000 genomes]
rs9450300	1.00[ASN][1000 genomes]
rs9450304	0.87[ASN][1000 genomes]
rs9450307	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9450308	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9450309	0.87[ASN][1000 genomes]
rs9450313	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6930790	NT5E	cis	Thyroid	GTEx
rs6930790	NT5E	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86192800-86221400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:86193000-86221200	Weak transcription	A549	lung
4	chr6:86193400-86219800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:86195000-86219800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:86196800-86221600	Weak transcription	Spleen	Spleen
7	chr6:86200600-86220400	Weak transcription	Psoas Muscle	Psoas
8	chr6:86200600-86221800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:86203400-86219800	Weak transcription	NHLF	lung
10	chr6:86205200-86219600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:86207000-86221600	Weak transcription	Lung	lung
12	chr6:86207200-86219800	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:86207200-86221200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:86207200-86221600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
16	chr6:86207400-86219600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:86207400-86221400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:86207400-86221600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:86207400-86221600	Weak transcription	Aorta	Aorta
20	chr6:86207400-86221600	Weak transcription	Fetal Stomach	stomach
21	chr6:86208600-86221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
23	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
24	chr6:86209000-86219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:86209000-86219800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:86209000-86221200	Weak transcription	Thymus	Thymus
27	chr6:86209000-86221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:86209000-86222600	Weak transcription	HepG2	liver
29	chr6:86209200-86219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:86209200-86221200	Weak transcription	NHEK	skin
31	chr6:86209200-86221400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:86209200-86222600	Weak transcription	Stomach Mucosa	stomach
33	chr6:86209200-86223000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:86209400-86219600	Weak transcription	HMEC	breast
35	chr6:86209400-86219600	Weak transcription	HUVEC	blood vessel
36	chr6:86209600-86219800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:86210000-86220000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:86210000-86221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:86210000-86221200	Weak transcription	Hela-S3	cervix
40	chr6:86210400-86219800	Weak transcription	Right Ventricle	heart
41	chr6:86210400-86220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:86211400-86246400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:86211600-86219600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:86212000-86224800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:86212000-86228600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr6:86212000-86246600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:86212200-86221600	Weak transcription	Fetal Intestine Small	intestine
48	chr6:86212600-86219600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:86212600-86219600	Weak transcription	Dnd41	blood
50	chr6:86212800-86220000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links