Variant report

Variant	rs1864395
Chromosome Location	chr10:43655697-43655698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43649752..43652450-chr10:43654182..43655742,2	K562	blood:
2	chr10:43642146..43644842-chr10:43653993..43656296,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12241923	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1254959	0.82[CHB][hapmap]
rs1254968	0.86[CHB][hapmap]
rs1272142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153156	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800861	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1864399	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2075910	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2075913	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435354	0.82[CHB][hapmap]
rs2435384	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2435385	0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2503841	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2503845	0.83[JPT][hapmap]
rs2503849	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2503865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2503866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505511	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2505512	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2505513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2505554	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742233	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2742234	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3004211	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3004214	0.89[CEU][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1864395	CSGALNACT2	cis	Skin Sun Exposed Lower leg	GTEx
rs1864395	CSGALNACT2	cis	Esophagus Muscularis	GTEx
rs1864395	CSGALNACT2	cis	Artery Tibial	GTEx
rs1864395	CSGALNACT2	cis	Nerve Tibial	GTEx
rs1864395	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs1864395	CSGALNACT2	cis	lung	GTEx
rs1864395	CSGALNACT2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
2	chr10:43641400-43657400	Weak transcription	A549	lung
3	chr10:43645600-43656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:43646600-43658400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:43647200-43656200	Weak transcription	Spleen	Spleen
6	chr10:43647200-43656400	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:43647200-43667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:43647400-43656200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:43647400-43656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:43647400-43656800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:43647400-43657200	Weak transcription	Left Ventricle	heart
12	chr10:43647400-43667800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:43647600-43659600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr10:43647600-43664000	Weak transcription	Fetal Brain Male	brain
15	chr10:43647600-43667000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr10:43649200-43657000	Weak transcription	Aorta	Aorta
17	chr10:43649200-43661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:43649600-43657600	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:43650400-43667600	Weak transcription	Brain Germinal Matrix	brain
20	chr10:43650800-43656200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:43651000-43671800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:43651200-43656800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:43652400-43656000	Weak transcription	Fetal Brain Female	brain
24	chr10:43652400-43657000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:43652400-43668600	Weak transcription	Fetal Heart	heart
26	chr10:43652600-43655800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:43652600-43655800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:43652600-43655800	Weak transcription	Fetal Thymus	thymus
29	chr10:43652600-43656000	Weak transcription	Thymus	Thymus
30	chr10:43652600-43656200	Weak transcription	Ovary	ovary
31	chr10:43652600-43656800	Weak transcription	Lung	lung
32	chr10:43652600-43657000	Weak transcription	Gastric	stomach
33	chr10:43652600-43658200	Weak transcription	Brain Angular Gyrus	brain
34	chr10:43652600-43667800	Weak transcription	Brain Substantia Nigra	brain
35	chr10:43652600-43669800	Weak transcription	Right Ventricle	heart
36	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
37	chr10:43652800-43656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:43652800-43657000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr10:43653000-43656200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:43653000-43656400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr10:43653000-43656800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:43653000-43668000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr10:43653200-43655800	Weak transcription	Primary T cells from cord blood	blood
44	chr10:43653200-43655800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:43653200-43656600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr10:43653200-43656800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:43653200-43663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:43653400-43667400	Weak transcription	Fetal Intestine Small	intestine
49	chr10:43653800-43657000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr10:43654200-43655800	Enhancers	Fetal Lung	lung

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