Variant report

Variant	rs9450731
Chromosome Location	chr6:88248476-88248477
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	chr6:88248391..88251882-chr6:88297586..88301251,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135336	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11965607	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663400	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13213729	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13220363	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35773999	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4330517	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4552702	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707380	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6911782	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7748693	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756133	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7768566	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs910267	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444515	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444529	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450725	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450727	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450730	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450757	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450759	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450765	0.82[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
rs9450731	SLC35A1	cis	multi-tissue	Pritchard
rs9450731	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
3	chr6:88219000-88249000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:88225000-88250800	Weak transcription	Stomach Mucosa	stomach
5	chr6:88227000-88250200	Weak transcription	Fetal Heart	heart
6	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
7	chr6:88228400-88250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:88228600-88249800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:88228600-88254000	Weak transcription	Gastric	stomach
11	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
12	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
14	chr6:88228800-88253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:88229400-88248800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:88229400-88248800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:88229400-88249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:88229600-88254000	Weak transcription	Brain Anterior Caudate	brain
22	chr6:88229600-88289000	Weak transcription	Lung	lung
23	chr6:88230000-88249200	Weak transcription	Fetal Lung	lung
24	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:88230600-88248600	Weak transcription	HMEC	breast
27	chr6:88230600-88249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:88230600-88254400	Weak transcription	Psoas Muscle	Psoas
29	chr6:88230800-88249000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:88230800-88249000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:88230800-88249800	Weak transcription	Ovary	ovary
32	chr6:88230800-88250600	Weak transcription	HSMMtube	muscle
33	chr6:88230800-88261600	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:88231200-88262800	Weak transcription	Brain Angular Gyrus	brain
35	chr6:88231200-88264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:88237000-88248600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:88237000-88249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:88237800-88248800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:88237800-88248800	Weak transcription	GM12878-XiMat	blood
40	chr6:88238000-88249000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:88238800-88253200	Weak transcription	K562	blood
42	chr6:88239200-88250400	Weak transcription	HUVEC	blood vessel
43	chr6:88240000-88253800	Weak transcription	Right Ventricle	heart
44	chr6:88240200-88249000	Weak transcription	A549	lung
45	chr6:88240200-88249200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:88240200-88250200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:88240200-88254000	Weak transcription	Colonic Mucosa	Colon
48	chr6:88240600-88248800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:88240600-88248800	Weak transcription	Fetal Kidney	kidney
50	chr6:88240600-88249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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