Variant report

Variant	rs2234358
Chromosome Location	chr3:45989044-45989045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1072755	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs11130080	0.82[ASN][1000 genomes]
rs12630101	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs12635494	0.87[ASN][1000 genomes]
rs12635657	0.81[ASN][1000 genomes]
rs13066048	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13091821	0.88[ASN][1000 genomes]
rs13091979	0.88[ASN][1000 genomes]
rs1392291	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532071	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546079	0.85[CEU][hapmap]
rs1552489	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs1552490	0.97[ASN][1000 genomes]
rs1601867	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17078449	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs17078495	0.81[ASN][1000 genomes]
rs1994488	0.97[ASN][1000 genomes]
rs1994489	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994490	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2054866	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.99[ASN][1000 genomes]
rs2248228	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2291470	0.80[ASN][1000 genomes]
rs35465473	0.99[ASN][1000 genomes]
rs35537559	0.81[ASN][1000 genomes]
rs3733100	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3733103	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs3774634	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs3774635	0.97[ASN][1000 genomes]
rs3774638	0.90[CHB][hapmap]
rs3774639	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs3796373	0.82[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs3796375	0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs3821884	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4535265	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs4682799	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]
rs4682800	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683148	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap]
rs4683149	0.86[ASN][1000 genomes]
rs4683152	0.91[ASN][1000 genomes]
rs4683153	0.81[EUR][1000 genomes]
rs4683154	0.94[ASN][1000 genomes]
rs4683156	0.99[ASN][1000 genomes]
rs4683157	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs59226168	0.81[ASN][1000 genomes]
rs62242796	0.81[ASN][1000 genomes]
rs67044455	0.81[ASN][1000 genomes]
rs6778896	0.81[ASN][1000 genomes]
rs6781121	0.81[EUR][1000 genomes]
rs6800954	0.80[CHB][hapmap];0.84[CHD][hapmap]
rs7129	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs730983	0.81[ASN][1000 genomes]
rs737452	0.81[ASN][1000 genomes]
rs751552	0.80[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs751553	0.80[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs9311380	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931704	0.81[ASN][1000 genomes]
rs936938	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs936939	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs9824253	0.96[ASN][1000 genomes]
rs9831315	0.82[CHB][hapmap]

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
rs2234358	CXCR6	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
5	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain
6	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:45981000-45990400	Weak transcription	Fetal Brain Female	brain
8	chr3:45981000-45993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
11	chr3:45982200-45999800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr3:45982800-46000800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:45984000-45994000	Weak transcription	HMEC	breast
15	chr3:45984200-45994200	Strong transcription	Liver	Liver
16	chr3:45984400-45998200	Strong transcription	Left Ventricle	heart
17	chr3:45984400-46000800	Weak transcription	Psoas Muscle	Psoas
18	chr3:45985800-45989400	Genic enhancers	Dnd41	blood
19	chr3:45986200-45989400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:45986200-45990600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:45986200-45993800	Strong transcription	Adipose Nuclei	Adipose
22	chr3:45986200-45998200	Strong transcription	Brain Substantia Nigra	brain
23	chr3:45986200-46006800	Strong transcription	Fetal Intestine Small	intestine
24	chr3:45986200-46007600	Strong transcription	Fetal Stomach	stomach
25	chr3:45986400-45990600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:45986400-45991400	Strong transcription	Right Ventricle	heart
27	chr3:45986400-45997000	Strong transcription	Pancreas	Pancrea
28	chr3:45986400-45997200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr3:45986400-46001400	Weak transcription	A549	lung
30	chr3:45986400-46006200	Strong transcription	Fetal Muscle Leg	muscle
31	chr3:45986400-46006800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:45986400-46007600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:45986600-45989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:45986600-45990600	Strong transcription	Primary T cells from cord blood	blood
37	chr3:45986600-45991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:45986600-45992000	Strong transcription	Gastric	stomach
39	chr3:45986600-45997000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr3:45986600-45997000	Strong transcription	Brain Angular Gyrus	brain
41	chr3:45986600-45997400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr3:45986600-46009000	Strong transcription	Primary B cells from cord blood	blood
43	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:45987000-45990000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr3:45987000-45990200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:45987000-45997600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:45987200-45989400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:45987200-45991000	Strong transcription	Colonic Mucosa	Colon

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