Variant report

Variant	rs4330517
Chromosome Location	chr6:88289693-88289694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88182686..88185163-chr6:88288656..88290504,2	K562	blood:
2	chr6:88285212..88293434-chr6:88297589..88302538,14	K562	blood:
3	chr6:88126441..88128032-chr6:88288832..88291183,2	MCF-7	breast:
4	chr6:88287850..88291294-chr6:88408676..88413224,5	MCF-7	breast:
5	chr6:88284821..88286391-chr6:88289308..88290910,2	K562	blood:
6	chr6:88285921..88288874-chr6:88289679..88293937,3	MCF-7	breast:
7	chr6:88287492..88290089-chr6:88410688..88412261,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11965607	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12663400	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13213729	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220363	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35773999	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4552702	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707380	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6911782	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748693	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756133	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7768566	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772351	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910267	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444515	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444529	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450725	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450727	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450730	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450731	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450757	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450759	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450765	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4330517	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs4330517	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
6	chr6:88256400-88295800	Weak transcription	Gastric	stomach
7	chr6:88263400-88291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:88264600-88291000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:88269600-88291400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:88272200-88297000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:88272400-88291000	Weak transcription	Fetal Brain Female	brain
12	chr6:88272400-88296000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:88272400-88297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:88272400-88297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:88272600-88291200	Weak transcription	HSMMtube	muscle
16	chr6:88272600-88292000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:88272800-88289800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:88272800-88291000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:88273000-88292000	Weak transcription	Colonic Mucosa	Colon
20	chr6:88273000-88296000	Weak transcription	Brain Substantia Nigra	brain
21	chr6:88273400-88290200	Weak transcription	HMEC	breast
22	chr6:88273600-88292400	Weak transcription	Hela-S3	cervix
23	chr6:88273600-88298200	Weak transcription	Fetal Kidney	kidney
24	chr6:88274000-88290800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:88274200-88295000	Weak transcription	NHLF	lung
26	chr6:88274400-88292200	Weak transcription	Fetal Lung	lung
27	chr6:88274800-88298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:88278800-88290200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:88278800-88290600	Weak transcription	HSMM	muscle
30	chr6:88278800-88297400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:88279400-88289800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:88279600-88291000	Weak transcription	Placenta	Placenta
33	chr6:88282000-88292200	Weak transcription	NHEK	skin
34	chr6:88283000-88292200	Weak transcription	Ovary	ovary
35	chr6:88283000-88296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:88283000-88297000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:88283000-88298600	Weak transcription	Aorta	Aorta
38	chr6:88284200-88290000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:88284400-88290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:88284400-88291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:88284400-88291600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:88284400-88293800	Weak transcription	Small Intestine	intestine
43	chr6:88284400-88298000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:88284800-88298200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:88285200-88293600	Weak transcription	Fetal Heart	heart
46	chr6:88285200-88297400	Weak transcription	Brain Anterior Caudate	brain
47	chr6:88285400-88289800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:88285400-88289800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:88285400-88290600	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:88285400-88291000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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