Variant report

Variant	rs13220363
Chromosome Location	chr6:88343844-88343845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11965607	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663400	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13213729	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35773999	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4330517	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4552702	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707380	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911782	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7748693	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756133	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768566	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772351	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910267	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444515	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444529	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450725	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450730	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450731	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450759	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450765	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13220363	SLC35A1	cis	multi-tissue	Pritchard
rs13220363	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs13220363	C6orf163	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
3	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
11	chr6:88312200-88371200	Weak transcription	NHEK	skin
12	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
14	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
16	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
18	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:88322600-88344800	Weak transcription	HMEC	breast
24	chr6:88322800-88344000	Weak transcription	Liver	Liver
25	chr6:88322800-88344800	Weak transcription	NH-A	brain
26	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:88323000-88344600	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:88323000-88344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
30	chr6:88323000-88366400	Weak transcription	A549	lung
31	chr6:88324000-88344000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:88324000-88347400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:88324000-88385000	Weak transcription	Gastric	stomach
35	chr6:88324200-88344800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:88324200-88346000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:88324200-88346200	Weak transcription	Fetal Brain Female	brain
38	chr6:88324200-88350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
42	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:88324400-88344600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:88324800-88344000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:88325200-88344800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:88325200-88344800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:88325400-88344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:88325400-88346200	Weak transcription	Left Ventricle	heart
50	chr6:88325400-88369200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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