Variant report

Variant	rs13213729
Chromosome Location	chr6:88249546-88249547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88240311..88242545-chr6:88248910..88250768,2	K562	blood:
2	chr6:88248391..88251882-chr6:88297586..88301251,3	MCF-7	breast:
3	chr6:88240458..88244227-chr6:88248910..88253061,5	K562	blood:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction
ENSG00000135336	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	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220363	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35773999	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4330517	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4552702	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707380	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6911782	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7748693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756133	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7768566	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7772351	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs910267	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444515	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444529	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450725	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450727	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450730	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450731	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450757	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450765	0.86[EUR][1000 genomes];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	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
rs13213729	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs13213729	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 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	chr6:88225000-88250800	Weak transcription	Stomach Mucosa	stomach
3	chr6:88227000-88250200	Weak transcription	Fetal Heart	heart
4	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
5	chr6:88228400-88250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:88228600-88249800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:88228600-88254000	Weak transcription	Gastric	stomach
9	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
10	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
12	chr6:88228800-88253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:88229600-88254000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:88229600-88289000	Weak transcription	Lung	lung
18	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
19	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:88230600-88254400	Weak transcription	Psoas Muscle	Psoas
21	chr6:88230800-88249800	Weak transcription	Ovary	ovary
22	chr6:88230800-88250600	Weak transcription	HSMMtube	muscle
23	chr6:88230800-88261600	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:88231200-88262800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:88231200-88264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:88238800-88253200	Weak transcription	K562	blood
27	chr6:88239200-88250400	Weak transcription	HUVEC	blood vessel
28	chr6:88240000-88253800	Weak transcription	Right Ventricle	heart
29	chr6:88240200-88250200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:88240200-88254000	Weak transcription	Colonic Mucosa	Colon
31	chr6:88240600-88250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:88240600-88254000	Weak transcription	Fetal Brain Female	brain
33	chr6:88240600-88268200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:88240800-88250200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:88240800-88250200	Weak transcription	NHEK	skin
36	chr6:88240800-88250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:88242400-88254000	Weak transcription	NHLF	lung
38	chr6:88244600-88253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:88244800-88249800	Weak transcription	Adipose Nuclei	Adipose
40	chr6:88244800-88250200	Weak transcription	Pancreas	Pancrea
41	chr6:88244800-88254000	Weak transcription	Left Ventricle	heart
42	chr6:88244800-88254400	Weak transcription	Aorta	Aorta
43	chr6:88246600-88249800	Strong transcription	Fetal Thymus	thymus
44	chr6:88246600-88252200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:88246600-88252200	Strong transcription	NHDF-Ad	bronchial
46	chr6:88246800-88251800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:88247000-88251800	Strong transcription	Fetal Intestine Large	intestine
48	chr6:88247200-88251000	Strong transcription	NH-A	brain
49	chr6:88248000-88249600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:88248000-88250200	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links