Variant report

Variant	rs835489
Chromosome Location	chr12:105062195-105062196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105058711..105060568-chr12:105060873..105063614,2	K562	blood:
2	chr12:105060606..105063528-chr12:105064614..105066569,2	K562	blood:
3	chr12:105061726..105063507-chr12:105070074..105072816,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2694406	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835490	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs835492	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs835493	0.80[ASN][1000 genomes]
rs856595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs864454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs835489	SLC5A8	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105038400-105062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:105038600-105062400	Weak transcription	HMEC	breast
3	chr12:105038600-105062800	Weak transcription	Esophagus	oesophagus
4	chr12:105038600-105063200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:105039200-105062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:105048000-105062400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:105049200-105062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:105051000-105065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:105051800-105062200	Weak transcription	Spleen	Spleen
10	chr12:105051800-105065000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:105053000-105062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:105055400-105062600	Genic enhancers	Dnd41	blood
13	chr12:105056000-105062600	Weak transcription	Small Intestine	intestine
14	chr12:105056200-105062400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:105057800-105063000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:105058000-105063200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:105058400-105062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:105059200-105063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:105059400-105062200	Weak transcription	GM12878-XiMat	blood
20	chr12:105059600-105063000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:105060200-105062400	Weak transcription	NH-A	brain
22	chr12:105060200-105068400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:105060400-105062600	Enhancers	Brain Hippocampus Middle	brain
24	chr12:105060400-105063000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:105060400-105063200	Enhancers	Brain Substantia Nigra	brain
26	chr12:105060400-105066800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:105060400-105067000	Enhancers	Pancreas	Pancrea
28	chr12:105060600-105062200	Enhancers	Rectal Smooth Muscle	rectum
29	chr12:105060600-105063200	Enhancers	Brain Anterior Caudate	brain
30	chr12:105060600-105064000	Enhancers	Fetal Brain Female	brain
31	chr12:105060600-105064400	Enhancers	A549	lung
32	chr12:105060600-105064600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:105060600-105066200	Enhancers	Fetal Lung	lung
34	chr12:105060600-105066600	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:105060800-105065800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:105060800-105067800	Enhancers	Placenta	Placenta
37	chr12:105061000-105062200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:105061000-105062200	Enhancers	Fetal Heart	heart
39	chr12:105061000-105062400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:105061000-105067800	Enhancers	Gastric	stomach
41	chr12:105061000-105068000	Enhancers	Fetal Muscle Leg	muscle
42	chr12:105061000-105068200	Enhancers	Fetal Stomach	stomach
43	chr12:105061200-105062200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:105061200-105063000	Enhancers	Right Ventricle	heart
45	chr12:105061200-105063200	Weak transcription	Liver	Liver
46	chr12:105061200-105066200	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:105061200-105067200	Enhancers	Adipose Nuclei	Adipose
48	chr12:105061200-105067200	Enhancers	Left Ventricle	heart
49	chr12:105061200-105067800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:105061200-105068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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