Variant report

Variant	rs13250181
Chromosome Location	chr8:19328766-19328767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19328304..19330762-chr8:19331773..19333660,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10105097	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10503653	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10888165	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11204044	0.85[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11204046	0.89[JPT][hapmap]
rs11204047	0.89[JPT][hapmap]
rs11204050	0.89[JPT][hapmap]
rs11204052	0.80[ASN][1000 genomes]
rs11777566	0.89[ASN][1000 genomes]
rs11778734	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11780475	0.82[ASN][1000 genomes]
rs11783263	0.89[JPT][hapmap]
rs11786904	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155539	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs12680768	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12682196	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13261442	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs13261732	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13261824	1.00[CHB][hapmap];0.90[YRI][hapmap]
rs13265751	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13266857	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13267801	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13275706	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276417	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs13280711	0.82[ASN][1000 genomes]
rs17128525	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs17479777	0.89[JPT][hapmap]
rs28671342	0.81[ASN][1000 genomes]
rs3185	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34221121	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35736969	0.81[ASN][1000 genomes]
rs3923920	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4073790	0.82[ASN][1000 genomes]
rs4073791	0.82[ASN][1000 genomes]
rs4244451	0.88[ASN][1000 genomes]
rs4244452	0.89[ASN][1000 genomes]
rs4244453	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4292704	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4311666	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4317590	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4319111	0.89[JPT][hapmap]
rs4339658	0.82[ASN][1000 genomes]
rs4379462	1.00[CHB][hapmap]
rs4409408	1.00[CHB][hapmap];0.95[YRI][hapmap]
rs4413788	0.89[JPT][hapmap]
rs4427190	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4442163	0.80[ASN][1000 genomes]
rs4455848	0.89[JPT][hapmap]
rs4483172	0.89[JPT][hapmap]
rs4484715	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4486225	1.00[CHB][hapmap]
rs4524812	0.89[ASN][1000 genomes]
rs4554481	0.89[JPT][hapmap]
rs4599829	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4631483	0.83[ASN][1000 genomes]
rs4921646	0.89[ASN][1000 genomes]
rs4921647	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4921648	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4921649	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4921651	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4921653	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921654	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921655	0.80[ASN][1000 genomes]
rs4921656	0.89[JPT][hapmap]
rs4921657	0.89[JPT][hapmap]
rs4922031	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4922034	0.88[ASN][1000 genomes]
rs4922035	1.00[ASN][1000 genomes]
rs4922036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4922044	0.89[JPT][hapmap]
rs4922045	0.89[JPT][hapmap]
rs4922046	0.89[JPT][hapmap]
rs4922047	0.89[JPT][hapmap]
rs4922048	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4922049	0.89[JPT][hapmap]
rs5013219	0.89[ASN][1000 genomes]
rs6586836	0.88[ASN][1000 genomes]
rs6586837	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6586838	0.88[ASN][1000 genomes]
rs6586839	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6586840	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6984449	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6984644	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6986388	1.00[ASN][1000 genomes]
rs6991941	0.89[JPT][hapmap]
rs6994352	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6998334	0.89[JPT][hapmap]
rs6999542	0.89[JPT][hapmap]
rs7002357	0.81[CHB][hapmap]
rs7005075	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7006155	1.00[ASN][1000 genomes]
rs7017776	0.89[JPT][hapmap]
rs7460541	0.80[ASN][1000 genomes]
rs7816777	0.89[JPT][hapmap]
rs7828025	1.00[CHB][hapmap]
rs7828197	0.82[ASN][1000 genomes]
rs7830404	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7839041	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9644631	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13250181	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19310600-19359600	Weak transcription	Ovary	ovary
2	chr8:19316200-19339200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr8:19318800-19332600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr8:19319400-19329000	Weak transcription	Placenta	Placenta
5	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
6	chr8:19319800-19332200	Weak transcription	Pancreas	Pancrea
7	chr8:19320200-19329200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:19321800-19329000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:19322400-19329000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:19324400-19334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:19325400-19335000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr8:19325800-19335800	Weak transcription	Primary B cells from cord blood	blood
13	chr8:19326200-19330400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr8:19326600-19332400	Enhancers	Primary T cells from cord blood	blood
15	chr8:19326800-19335000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr8:19327200-19329200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr8:19327400-19329000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:19327400-19329400	Enhancers	A549	lung
19	chr8:19327800-19329000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr8:19327800-19329000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr8:19328000-19329000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr8:19328000-19332600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr8:19328000-19337800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:19328200-19332400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:19328200-19334000	Weak transcription	Right Atrium	heart
26	chr8:19328200-19334200	Weak transcription	Left Ventricle	heart
27	chr8:19328600-19328800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr8:19328600-19331200	Enhancers	HUVEC	blood vessel

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