Variant report

Variant	rs7129
Chromosome Location	chr3:45959759-45959760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45957988..45959492-chr3:45959750..45961379,2	K562	blood:
2	chr3:45958439..45960531-chr3:46002605..46005170,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1072755	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130080	0.88[CEU][hapmap]
rs12495073	0.84[CEU][hapmap]
rs12630101	0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635494	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635657	0.90[CEU][hapmap]
rs12639598	0.88[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs13066048	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091821	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091979	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532071	0.84[ASN][1000 genomes]
rs1552489	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552490	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1601867	0.82[ASN][1000 genomes]
rs1994488	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1994489	0.84[ASN][1000 genomes]
rs1994490	0.85[MEX][hapmap]
rs2054866	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171530	0.96[ASN][1000 genomes]
rs2234358	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs2248228	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291470	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35465473	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3733103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774634	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774635	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774639	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796373	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3796375	0.88[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs3821884	0.81[MEX][hapmap]
rs4535265	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682799	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs4682800	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs4683147	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4683148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683149	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683152	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683154	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683156	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683157	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6800954	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs730983	0.88[CEU][hapmap]
rs737452	0.88[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs751552	0.88[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs751553	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs9311380	0.84[ASN][1000 genomes]
rs936938	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9824253	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7129	UBA7	cis	parietal	SCAN
rs7129	DALRD3	cis	cerebellum	SCAN
rs7129	SS18L2	cis	parietal	SCAN
rs7129	CXCR6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
3	chr3:45940000-45959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:45941400-45960000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:45943600-45961200	Weak transcription	Gastric	stomach
7	chr3:45946200-45960400	Weak transcription	Aorta	Aorta
8	chr3:45947000-45960200	Weak transcription	Lung	lung
9	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:45948800-45960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:45949800-45962600	Weak transcription	HepG2	liver
14	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:45950200-45959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:45950200-45960000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:45950200-45960400	Weak transcription	Pancreas	Pancrea
18	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
19	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
20	chr3:45953200-45960800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:45953400-45959800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:45955800-45960000	Weak transcription	Fetal Intestine Large	intestine
23	chr3:45956600-45960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:45956800-45961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:45957400-45960800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:45957400-45961600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:45957600-45960000	Weak transcription	Fetal Lung	lung
29	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:45957800-45960000	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:45957800-45960200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:45957800-45960200	Weak transcription	Left Ventricle	heart
33	chr3:45957800-45960800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:45957800-45961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:45957800-45961400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
44	chr3:45957800-45969000	Weak transcription	K562	blood
45	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:45958000-45959800	Enhancers	GM12878-XiMat	blood
47	chr3:45958000-45960000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:45958000-45960000	Weak transcription	Placenta	Placenta
49	chr3:45958000-45960200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:45958000-45960200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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