Variant report

Variant	rs28491635
Chromosome Location	chr8:19354292-19354293
allele	C/G/T
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	MYC	chr8:19354114-19354333	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr8:19354152-19354320	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19352728..19355401-chr8:19358201..19360523,2	K562	blood:

Variant related genes	Relation type
CSGALNACT1	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10087317	1.00[AMR][1000 genomes]
rs10087663	1.00[AMR][1000 genomes]
rs10088450	1.00[AMR][1000 genomes]
rs10090079	0.83[AFR][1000 genomes]
rs10094142	1.00[AMR][1000 genomes]
rs10096485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10096490	1.00[AMR][1000 genomes]
rs10096638	1.00[AMR][1000 genomes]
rs10097851	1.00[AMR][1000 genomes]
rs10101907	1.00[AMR][1000 genomes]
rs10104615	1.00[AMR][1000 genomes]
rs10104968	1.00[AMR][1000 genomes]
rs10106180	1.00[AMR][1000 genomes]
rs10106270	1.00[AMR][1000 genomes]
rs10107181	1.00[AMR][1000 genomes]
rs10109345	1.00[AMR][1000 genomes]
rs10481442	0.83[AFR][1000 genomes]
rs17128428	0.83[AFR][1000 genomes]
rs17128520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17128532	1.00[AMR][1000 genomes]
rs17128535	1.00[AMR][1000 genomes]
rs17128545	1.00[AMR][1000 genomes]
rs17128641	1.00[AMR][1000 genomes]
rs17128662	1.00[AMR][1000 genomes]
rs17128691	1.00[AMR][1000 genomes]
rs17128714	1.00[AMR][1000 genomes]
rs17128743	1.00[AMR][1000 genomes]
rs28415838	1.00[AMR][1000 genomes]
rs28427117	1.00[AMR][1000 genomes]
rs28457744	1.00[AMR][1000 genomes]
rs28558362	0.83[AFR][1000 genomes]
rs28578312	1.00[AMR][1000 genomes]
rs28607676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661517	1.00[AMR][1000 genomes]
rs28713671	1.00[AMR][1000 genomes]
rs28738093	1.00[AMR][1000 genomes]
rs28742998	1.00[AMR][1000 genomes]
rs7817946	1.00[AMR][1000 genomes]
rs7821215	1.00[AMR][1000 genomes]
rs7821389	1.00[AMR][1000 genomes]
rs7821612	1.00[AMR][1000 genomes]
rs7824941	1.00[AMR][1000 genomes]
rs7839912	1.00[AMR][1000 genomes]
rs7840172	1.00[AMR][1000 genomes]
rs7843893	1.00[AMR][1000 genomes]
rs9325858	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv890624	chr8:19319061-19456270	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19310600-19359600	Weak transcription	Ovary	ovary
2	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
3	chr8:19333400-19362200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
5	chr8:19346400-19357000	Weak transcription	Fetal Lung	lung
6	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:19348200-19364000	Weak transcription	Brain Hippocampus Middle	brain
8	chr8:19348200-19367400	Weak transcription	Fetal Brain Female	brain
9	chr8:19348600-19359000	Weak transcription	Fetal Brain Male	brain
10	chr8:19349800-19355000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:19350200-19362800	Weak transcription	Gastric	stomach
12	chr8:19351200-19369000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr8:19352000-19354400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:19352000-19354600	Weak transcription	Right Ventricle	heart
15	chr8:19352000-19356800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr8:19352400-19356600	Enhancers	Fetal Thymus	thymus
17	chr8:19352400-19357400	Weak transcription	Hela-S3	cervix
18	chr8:19353200-19354400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:19353200-19354600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr8:19353200-19358000	Weak transcription	Primary B cells from cord blood	blood
21	chr8:19353200-19362200	Weak transcription	Adipose Nuclei	Adipose
22	chr8:19353400-19354400	Weak transcription	Brain Angular Gyrus	brain
23	chr8:19353400-19354400	Weak transcription	Placenta	Placenta
24	chr8:19353400-19355600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr8:19353400-19359600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr8:19353400-19367600	Weak transcription	Brain Anterior Caudate	brain
27	chr8:19353400-19367600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr8:19353600-19355200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr8:19353600-19355400	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr8:19353800-19354600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:19353800-19354600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr8:19353800-19354600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr8:19353800-19354600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr8:19353800-19354800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:19353800-19355400	Bivalent Enhancer	Dnd41	blood
36	chr8:19353800-19356400	Enhancers	Thymus	Thymus
37	chr8:19354000-19354400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr8:19354000-19354600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr8:19354000-19354600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr8:19354000-19354600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr8:19354000-19354800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr8:19354000-19354800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr8:19354000-19355000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr8:19354000-19355000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr8:19354000-19355400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr8:19354000-19356000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr8:19354000-19357400	Enhancers	Left Ventricle	heart
48	chr8:19354200-19354400	Enhancers	Brain Substantia Nigra	brain
49	chr8:19354200-19354600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr8:19354200-19354600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links