Variant report

Variant	rs4682799
Chromosome Location	chr3:45993606-45993607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45992659..45994641-chr3:46028942..46030792,2	K562	blood:
2	chr3:45992876..45995243-chr3:45997512..46000332,2	K562	blood:
3	chr3:45992901..45995659-chr3:45998923..46000689,2	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1072755	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11130080	0.81[ASN][1000 genomes]
rs12630101	0.81[CHD][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs12635494	0.86[ASN][1000 genomes]
rs12639598	0.82[ASN][1000 genomes]
rs13066048	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13091821	0.91[ASN][1000 genomes]
rs13091979	0.91[ASN][1000 genomes]
rs1392291	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1532071	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546079	0.85[CEU][hapmap]
rs1552489	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1552490	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1601867	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17078449	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs1994488	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1994489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994490	0.96[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054866	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2171530	0.82[ASN][1000 genomes]
rs2234358	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248228	0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2291470	0.83[ASN][1000 genomes]
rs35465473	0.98[ASN][1000 genomes]
rs3733100	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733103	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs3774634	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3774635	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3774638	0.86[CHB][hapmap]
rs3774639	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs3796373	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs3796375	0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs3821884	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4535265	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs4682800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683148	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs4683149	0.89[ASN][1000 genomes]
rs4683152	0.93[ASN][1000 genomes]
rs4683153	0.81[EUR][1000 genomes]
rs4683154	0.93[ASN][1000 genomes]
rs4683156	0.97[ASN][1000 genomes]
rs4683157	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs62242787	0.81[ASN][1000 genomes]
rs6781121	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs6800954	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs7129	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs751552	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs751553	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs9311380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs936939	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs9824253	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9831315	0.86[CHB][hapmap];0.82[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4682799	CXCR6	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
6	chr3:45982200-45999800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:45982800-46000800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:45984000-45994000	Weak transcription	HMEC	breast
10	chr3:45984200-45994200	Strong transcription	Liver	Liver
11	chr3:45984400-45998200	Strong transcription	Left Ventricle	heart
12	chr3:45984400-46000800	Weak transcription	Psoas Muscle	Psoas
13	chr3:45986200-45993800	Strong transcription	Adipose Nuclei	Adipose
14	chr3:45986200-45998200	Strong transcription	Brain Substantia Nigra	brain
15	chr3:45986200-46006800	Strong transcription	Fetal Intestine Small	intestine
16	chr3:45986200-46007600	Strong transcription	Fetal Stomach	stomach
17	chr3:45986400-45997000	Strong transcription	Pancreas	Pancrea
18	chr3:45986400-45997200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr3:45986400-46001400	Weak transcription	A549	lung
20	chr3:45986400-46006200	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:45986400-46006800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:45986400-46007600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:45986600-45997000	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr3:45986600-45997000	Strong transcription	Brain Angular Gyrus	brain
27	chr3:45986600-45997400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr3:45986600-46009000	Strong transcription	Primary B cells from cord blood	blood
29	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:45987000-45997600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:45987600-45998200	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr3:45987600-46002000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:45987600-46007800	Strong transcription	K562	blood
39	chr3:45987800-45995600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:45987800-45997400	Strong transcription	Brain Anterior Caudate	brain
41	chr3:45987800-45997600	Strong transcription	Brain Hippocampus Middle	brain
42	chr3:45987800-46001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:45987800-46012200	Strong transcription	HepG2	liver
44	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:45988000-45994200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:45988000-45997000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:45988000-45997000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:45988000-45997600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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