Variant report

Variant	rs4841294
Chromosome Location	chr8:10105068-10105069
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10087391	1.00[ASN][1000 genomes]
rs10089339	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10090440	1.00[ASN][1000 genomes]
rs10097184	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10111917	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10112446	1.00[ASN][1000 genomes]
rs10903321	1.00[CHB][hapmap]
rs11249975	1.00[ASN][1000 genomes]
rs11774220	1.00[CHB][hapmap]
rs11774276	1.00[ASN][1000 genomes]
rs11776035	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11776973	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780122	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11783705	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12156030	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156387	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678938	1.00[ASN][1000 genomes]
rs13252589	1.00[CHB][hapmap]
rs13258409	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13263482	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13263803	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13272793	1.00[CHB][hapmap]
rs13275453	1.00[ASN][1000 genomes]
rs13279701	1.00[CHB][hapmap]
rs1484641	1.00[CHB][hapmap]
rs17151658	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151675	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151684	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151697	1.00[ASN][1000 genomes]
rs17151699	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151713	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151728	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151741	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151745	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151748	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17690549	1.00[CHB][hapmap]
rs17693945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694485	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707665	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17707988	1.00[CHB][hapmap]
rs17708090	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17708114	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17746227	1.00[CHB][hapmap]
rs17746245	1.00[CHB][hapmap]
rs17747335	1.00[CHB][hapmap]
rs17750324	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751178	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976071	1.00[ASN][1000 genomes]
rs2272597	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2272598	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28507813	1.00[ASN][1000 genomes]
rs28587507	1.00[ASN][1000 genomes]
rs28611339	1.00[ASN][1000 genomes]
rs28870492	1.00[ASN][1000 genomes]
rs34487797	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34919878	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35437983	1.00[ASN][1000 genomes]
rs4240640	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4394398	1.00[ASN][1000 genomes]
rs4840467	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840476	1.00[ASN][1000 genomes]
rs4841295	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841296	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs4841312	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55836143	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55968335	1.00[ASN][1000 genomes]
rs56408109	1.00[ASN][1000 genomes]
rs59119294	1.00[ASN][1000 genomes]
rs66666973	1.00[ASN][1000 genomes]
rs67773656	1.00[ASN][1000 genomes]
rs6983870	0.80[MEX][hapmap]
rs6985941	1.00[CHB][hapmap]
rs6994060	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6997224	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7014570	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73193549	1.00[ASN][1000 genomes]
rs7822745	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7834714	1.00[ASN][1000 genomes]
rs7835507	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7835960	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7840347	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1028650	chr8:10101815-10178537	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4841294	CLDN23	cis	multi-tissue	Pritchard
rs4841294	AMAC1L2	cis	parietal	SCAN
rs4841294	BLK	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10095400-10111600	Weak transcription	Primary T cells from cord blood	blood
2	chr8:10096000-10128000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:10096200-10107200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr8:10103200-10109600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr8:10103200-10117800	Weak transcription	Pancreas	Pancrea
6	chr8:10103400-10105200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:10103400-10106400	Weak transcription	Esophagus	oesophagus
8	chr8:10103400-10107800	Weak transcription	Brain Angular Gyrus	brain
9	chr8:10103400-10108000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr8:10103400-10110000	Weak transcription	Lung	lung
11	chr8:10103400-10110000	Weak transcription	Psoas Muscle	Psoas
12	chr8:10103400-10111400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr8:10103400-10111600	Weak transcription	Left Ventricle	heart
14	chr8:10103400-10112000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:10103400-10115800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr8:10103600-10105200	Enhancers	HUVEC	blood vessel
17	chr8:10103600-10106400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:10103600-10110600	Weak transcription	Ovary	ovary
19	chr8:10103600-10111400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr8:10103600-10111600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr8:10103600-10115600	Weak transcription	Fetal Intestine Small	intestine
22	chr8:10103600-10118000	Weak transcription	Gastric	stomach
23	chr8:10103600-10122600	Weak transcription	Spleen	Spleen
24	chr8:10104000-10124600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:10104600-10106200	Enhancers	Fetal Brain Female	brain
26	chr8:10104800-10105600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr8:10104800-10111400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:10105000-10106200	Enhancers	Fetal Brain Male	brain
29	chr8:10105000-10108400	Enhancers	Brain Germinal Matrix	brain

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