Variant report

Variant	rs12639598
Chromosome Location	chr3:46016464-46016465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46011530..46014566-chr3:46015264..46018457,3	K562	blood:
2	chr3:46015505..46018391-chr3:46024106..46026296,2	K562	blood:
3	chr3:46014022..46017742-chr3:46018515..46020350,3	MCF-7	breast:
4	chr3:46009297..46011383-chr3:46015916..46019063,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1072755	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11130080	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485978	0.82[JPT][hapmap]
rs12495073	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12630101	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12635494	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060901	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13066048	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13073861	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs13091821	0.80[EUR][1000 genomes]
rs13091979	0.80[EUR][1000 genomes]
rs1392290	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1392291	0.89[ASN][1000 genomes]
rs1491959	0.82[JPT][hapmap]
rs1532071	0.82[ASN][1000 genomes]
rs1546077	0.82[JPT][hapmap]
rs1552489	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1552490	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17078495	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994488	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1994489	0.82[ASN][1000 genomes]
rs1994490	0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs2054866	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2131091	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2248228	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2373154	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs28808964	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35465473	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35537559	0.98[ASN][1000 genomes]
rs3733097	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733100	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3733103	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs3774634	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs3774635	0.83[EUR][1000 genomes]
rs3774639	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3796375	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796376	0.82[CHD][hapmap]
rs3821883	0.81[ASN][1000 genomes]
rs3821884	0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3851347	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4234452	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4535265	0.96[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682799	0.82[ASN][1000 genomes]
rs4682800	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4682810	0.82[JPT][hapmap]
rs4683148	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs4683149	0.82[EUR][1000 genomes]
rs4683152	0.82[EUR][1000 genomes]
rs4683154	0.82[EUR][1000 genomes]
rs4683156	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4683157	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59226168	0.98[ASN][1000 genomes]
rs60539039	0.87[ASN][1000 genomes]
rs62242796	0.98[ASN][1000 genomes]
rs67044455	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764042	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6778896	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780163	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6781668	0.81[ASN][1000 genomes]
rs6795629	0.82[JPT][hapmap]
rs6805094	0.81[ASN][1000 genomes]
rs6809381	0.81[CHB][hapmap]
rs7129	0.88[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs730983	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737452	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751552	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751553	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623460	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7643426	0.81[CHB][hapmap]
rs9311380	0.82[ASN][1000 genomes]
rs931704	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936938	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9824253	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9824886	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9831315	0.92[CEU][hapmap]

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	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	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
4	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12639598	CXCR6	cis	parietal	SCAN
rs12639598	NCKIPSD	cis	parietal	SCAN
rs12639598	UBA7	cis	parietal	SCAN
rs12639598	CCDC71	cis	cerebellum	SCAN
rs12639598	CDC25A	cis	cerebellum	SCAN
rs12639598	CXCR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
2	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:45990600-46017200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:45991200-46017400	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr3:45996200-46025400	Strong transcription	Liver	Liver
13	chr3:45999400-46018200	Strong transcription	Fetal Lung	lung
14	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:46002200-46018600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:46002600-46025000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:46002600-46027200	Weak transcription	A549	lung
18	chr3:46007800-46024200	Weak transcription	Fetal Kidney	kidney
19	chr3:46008600-46026400	Strong transcription	Hela-S3	cervix
20	chr3:46009000-46027800	Weak transcription	Fetal Brain Male	brain
21	chr3:46009200-46017000	Weak transcription	Stomach Mucosa	stomach
22	chr3:46009600-46018000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:46010200-46021000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:46010200-46022600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:46010200-46024200	Strong transcription	Left Ventricle	heart
26	chr3:46010200-46027000	Weak transcription	Fetal Brain Female	brain
27	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:46010600-46017400	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:46010600-46020800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:46010800-46022400	Weak transcription	Fetal Heart	heart
32	chr3:46011400-46020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:46012000-46020800	Weak transcription	Ovary	ovary
34	chr3:46012800-46016600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:46013000-46017200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr3:46013000-46019200	Strong transcription	Adipose Nuclei	Adipose
37	chr3:46013000-46026200	Weak transcription	Brain Germinal Matrix	brain
38	chr3:46013200-46017000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:46013200-46017600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:46013600-46017600	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr3:46013600-46017800	Genic enhancers	Thymus	Thymus
42	chr3:46013600-46018000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr3:46013600-46021000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:46013600-46023000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:46013600-46025000	Strong transcription	Fetal Intestine Small	intestine
46	chr3:46013600-46025400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:46013600-46025600	Strong transcription	Fetal Stomach	stomach
48	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
49	chr3:46013800-46016800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:46013800-46017600	Genic enhancers	Dnd41	blood

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