Variant report

Variant	rs9450725
Chromosome Location	chr6:88234543-88234544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213729	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220363	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35773999	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4330517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4552702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707380	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6911782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7748693	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756133	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7768566	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772351	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs910267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444515	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444529	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450727	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450730	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450731	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450756	0.82[CHB][hapmap]
rs9450757	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450759	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450765	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS 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	18 gene(s)	inside rSNPs	diseases
2	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450725	SLC35A1	cis	multi-tissue	Pritchard
rs9450725	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88194000-88249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:88207200-88242600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr6:88210200-88240600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:88210400-88235000	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr6:88210800-88235000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:88211000-88235000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:88211000-88235200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:88211000-88241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:88212000-88245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:88214200-88244400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:88214800-88235400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:88215200-88235000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:88215200-88235000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:88215800-88240800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
16	chr6:88218200-88235200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:88218600-88236200	Strong transcription	Fetal Intestine Large	intestine
18	chr6:88219000-88249000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:88220000-88244200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:88221000-88235000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:88221000-88235400	Strong transcription	HepG2	liver
22	chr6:88221000-88240800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:88225000-88250800	Weak transcription	Stomach Mucosa	stomach
24	chr6:88227000-88250200	Weak transcription	Fetal Heart	heart
25	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
26	chr6:88228000-88236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:88228400-88239400	Weak transcription	Fetal Brain Female	brain
28	chr6:88228400-88250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:88228600-88236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:88228600-88239000	Weak transcription	Right Ventricle	heart
32	chr6:88228600-88239200	Weak transcription	A549	lung
33	chr6:88228600-88239600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:88228600-88239600	Weak transcription	Brain Germinal Matrix	brain
35	chr6:88228600-88244200	Weak transcription	Aorta	Aorta
36	chr6:88228600-88244400	Weak transcription	Fetal Stomach	stomach
37	chr6:88228600-88249800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:88228600-88254000	Weak transcription	Gastric	stomach
39	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
40	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
42	chr6:88228800-88235400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:88228800-88239400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:88228800-88240000	Weak transcription	NHLF	lung
45	chr6:88228800-88244400	Weak transcription	Pancreas	Pancrea
46	chr6:88228800-88253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:88229000-88239800	Weak transcription	Thymus	Thymus
49	chr6:88229400-88248800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:88229400-88248800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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