Variant report

Variant	rs12529993
Chromosome Location	chr6:88283420-88283421
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:88283272-88283843	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:88283404-88283666	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:88283102-88283794	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:88283059-88283856	HepG2	liver:	n/a	n/a
5	CEBPB	chr6:88283118-88283477	HepG2	liver:	n/a	chr6:88283310-88283321 chr6:88283267-88283278
6	FOXA2	chr6:88283000-88283659	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:88283021-88283724	HepG2	liver:	n/a	n/a
8	EP300	chr6:88283090-88283757	HepG2	liver:	n/a	chr6:88283526-88283536 chr6:88283436-88283443
9	EP300	chr6:88283244-88283699	HepG2	liver:	n/a	chr6:88283526-88283536 chr6:88283436-88283443
10	HNF4G	chr6:88283380-88283609	HepG2	liver:	n/a	n/a
11	FOXA2	chr6:88283398-88283784	HepG2	liver:	n/a	n/a
12	ELF1	chr6:88283320-88283543	HepG2	liver:	n/a	chr6:88283436-88283445 chr6:88283435-88283446 chr6:88283435-88283446

No.	Distal block	Cell Line	Cell type
1	chr6:88282649..88284478-chr6:88285308..88287961,2	MCF-7	breast:
2	chr6:88279883..88284316-chr6:88297696..88301610,6	MCF-7	breast:
3	chr6:88276251..88278746-chr6:88282738..88284494,3	MCF-7	breast:
4	chr6:88281663..88283868-chr6:88287306..88289197,2	K562	blood:
5	chr6:88280277..88282266-chr6:88282355..88283932,2	MCF-7	breast:
6	chr6:88282635..88286754-chr6:88286787..88288868,3	MCF-7	breast:

Variant related genes	Relation type
RARS2	TF binding region
ENSG00000135336	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11970493	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12530371	0.95[ASN][1000 genomes]
rs34513746	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4132446	0.86[ASN][1000 genomes]
rs4354121	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58305152	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454634	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6914244	0.92[ASN][1000 genomes]
rs7759462	0.85[ASN][1000 genomes]
rs9444511	0.85[ASN][1000 genomes]
rs9444513	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9444514	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9444516	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444521	0.86[ASN][1000 genomes]
rs9450728	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9450729	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9450734	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9450735	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450740	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450741	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450743	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450749	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9450750	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9450751	0.90[ASN][1000 genomes]
rs9450756	0.92[ASN][1000 genomes]
rs9450760	0.88[ASN][1000 genomes]
rs9450763	0.86[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	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
2	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
3	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
4	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
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12529993	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
2	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
3	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
5	chr6:88229600-88289000	Weak transcription	Lung	lung
6	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:88251200-88284800	Weak transcription	Stomach Mucosa	stomach
8	chr6:88254200-88283600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:88256000-88284000	Weak transcription	Psoas Muscle	Psoas
10	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
11	chr6:88256400-88295800	Weak transcription	Gastric	stomach
12	chr6:88263400-88291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:88264600-88291000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:88269600-88291400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:88271400-88288200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:88271600-88288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:88271600-88288800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:88272200-88297000	Weak transcription	Brain Germinal Matrix	brain
19	chr6:88272400-88284800	Weak transcription	Pancreas	Pancrea
20	chr6:88272400-88289200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:88272400-88291000	Weak transcription	Fetal Brain Female	brain
22	chr6:88272400-88296000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:88272400-88297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:88272400-88297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:88272600-88291200	Weak transcription	HSMMtube	muscle
26	chr6:88272600-88292000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:88272800-88283800	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:88272800-88289800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:88272800-88291000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:88273000-88283600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:88273000-88284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:88273000-88292000	Weak transcription	Colonic Mucosa	Colon
33	chr6:88273000-88296000	Weak transcription	Brain Substantia Nigra	brain
34	chr6:88273400-88290200	Weak transcription	HMEC	breast
35	chr6:88273600-88283600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:88273600-88292400	Weak transcription	Hela-S3	cervix
37	chr6:88273600-88298200	Weak transcription	Fetal Kidney	kidney
38	chr6:88274000-88283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:88274000-88283800	Weak transcription	Brain Anterior Caudate	brain
40	chr6:88274000-88288800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:88274000-88288800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:88274000-88290800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:88274200-88283600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:88274200-88283800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:88274200-88284200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:88274200-88284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:88274200-88288800	Weak transcription	NHDF-Ad	bronchial
48	chr6:88274200-88295000	Weak transcription	NHLF	lung
49	chr6:88274400-88284400	Weak transcription	Dnd41	blood
50	chr6:88274400-88289000	Weak transcription	Fetal Muscle Leg	muscle

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