Variant report

Variant	rs4611808
Chromosome Location	chr3:51469107-51469108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055429	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10865970	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130293	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11721253	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs1383251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480353	1.00[CEU][hapmap]
rs1480354	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480357	0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs1480358	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap]
rs1542574	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1552072	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs1552073	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs1552074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051734	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17051762	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2127655	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219890	1.00[CEU][hapmap]
rs4687568	0.84[AMR][1000 genomes]
rs4687569	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687734	0.84[AMR][1000 genomes]
rs4687800	0.83[EUR][1000 genomes]
rs4974095	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs4974104	1.00[CEU][hapmap]
rs4974105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974106	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974109	0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs6445620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6445622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs6445628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445727	0.83[EUR][1000 genomes]
rs6445791	0.81[AMR][1000 genomes]
rs6773260	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6787312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs6793900	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6809155	0.86[AMR][1000 genomes]
rs7372658	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs751075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633708	0.84[CEU][hapmap]
rs7648012	0.92[CEU][hapmap]
rs9311469	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855442	0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs9878100	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
2	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv3369762	chr3:51449727-51469314	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3444499	chr3:51449727-51469614	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4611808	HYAL2	cis	parietal	SCAN
rs4611808	TEX264	cis	Artery Tibial	GTEx
rs4611808	HEMK1	cis	cerebellum	SCAN
rs4611808	TEX264	cis	Esophagus Muscularis	GTEx
rs4611808	MST1	cis	cerebellum	SCAN
rs4611808	TEX264	cis	Nerve Tibial	GTEx
rs4611808	IQCF2	cis	parietal	SCAN
rs4611808	NCKIPSD	cis	cerebellum	SCAN
rs4611808	PARP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51431400-51471200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
3	chr3:51434000-51475600	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:51434600-51471000	Weak transcription	Stomach Mucosa	stomach
6	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:51446200-51471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:51451200-51476800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:51451400-51469600	Strong transcription	Fetal Stomach	stomach
14	chr3:51458000-51474800	Weak transcription	K562	blood
15	chr3:51458200-51474400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:51458200-51474600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:51458200-51475200	Weak transcription	NHLF	lung
18	chr3:51458200-51475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:51458200-51477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:51458200-51478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:51458200-51489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
23	chr3:51458400-51473000	Weak transcription	Pancreas	Pancrea
24	chr3:51458400-51474200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:51458400-51475400	Weak transcription	Gastric	stomach
26	chr3:51458400-51500200	Weak transcription	Psoas Muscle	Psoas
27	chr3:51458800-51503800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:51460000-51472400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:51460000-51475400	Weak transcription	Aorta	Aorta
30	chr3:51460200-51474000	Weak transcription	A549	lung
31	chr3:51461800-51478000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:51462400-51478200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:51462600-51470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:51462600-51476000	Strong transcription	Primary T cells from cord blood	blood
35	chr3:51462600-51477000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:51462600-51477200	Strong transcription	Placenta	Placenta
37	chr3:51462600-51477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:51462600-51477400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:51462800-51475400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:51463000-51469200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr3:51463000-51469400	Strong transcription	Adipose Nuclei	Adipose
42	chr3:51463000-51477200	Strong transcription	Liver	Liver
43	chr3:51463000-51477600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:51463200-51469200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:51463200-51470400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:51463200-51470600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:51463200-51471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:51463200-51478000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:51463400-51470400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:51463400-51470600	Strong transcription	Duodenum Mucosa	Duodenum

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