Variant report

Variant	rs6447670
Chromosome Location	chr4:48890460-48890461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10517231	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729065	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11733534	0.85[AFR][1000 genomes]
rs11734191	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11737706	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13146034	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13152270	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1455940	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1463365	0.87[ASN][1000 genomes]
rs2085292	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289065	0.90[ASN][1000 genomes]
rs2290516	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34730980	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3761729	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4695407	0.88[AFR][1000 genomes]
rs724598	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7672280	0.84[EUR][1000 genomes]
rs7685360	0.89[ASN][1000 genomes]
rs7687992	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9291326	0.90[AFR][1000 genomes]
rs9637562	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9997920	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6447670	SLC10A4	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:48860800-48892000	Weak transcription	Thymus	Thymus
3	chr4:48860800-48892800	Weak transcription	Aorta	Aorta
4	chr4:48860800-48892800	Weak transcription	Left Ventricle	heart
5	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:48863600-48892000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:48873200-48892000	Weak transcription	Primary T cells from cord blood	blood
9	chr4:48874000-48893600	Weak transcription	Pancreas	Pancrea
10	chr4:48875000-48892000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:48877400-48891800	Weak transcription	Fetal Brain Female	brain
12	chr4:48877800-48897000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
14	chr4:48880400-48892800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:48880600-48894800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:48882200-48892400	Weak transcription	Primary B cells from cord blood	blood
17	chr4:48884800-48891800	Weak transcription	Fetal Thymus	thymus
18	chr4:48885000-48892600	Weak transcription	Dnd41	blood
19	chr4:48885600-48891600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:48886000-48892000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:48886200-48892000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:48887200-48904200	Weak transcription	Esophagus	oesophagus
23	chr4:48887400-48893200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:48887800-48891800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:48887800-48892000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:48887800-48893400	Weak transcription	HMEC	breast
27	chr4:48887800-48903800	Weak transcription	Placenta	Placenta
28	chr4:48888000-48892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:48888000-48892800	Weak transcription	NHEK	skin
30	chr4:48889200-48892000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:48889800-48891800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr4:48890000-48891800	Weak transcription	Liver	Liver
33	chr4:48890200-48892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:48890200-48892000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:48890400-48892000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:48890400-48892000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:48890400-48892600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:48890400-48894800	Weak transcription	Ovary	ovary

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