Variant report

Variant	rs10863983
Chromosome Location	chr1:212800886-212800887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BATF3-2	chr1:212800569-212805905	XLOC_001195
2	lnc-BATF3-2	chr1:212800582-212804801	XLOC_001195

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3122710	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs3122713	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3125297	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3795842	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9429889	0.85[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10863983	CD46	cis	parietal	SCAN
rs10863983	C1orf227	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212785000-212801000	Weak transcription	Fetal Heart	heart
2	chr1:212790400-212802400	Weak transcription	Thymus	Thymus
3	chr1:212793000-212801200	Weak transcription	Fetal Lung	lung
4	chr1:212793000-212803200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:212793200-212803200	Weak transcription	Spleen	Spleen
6	chr1:212793600-212803200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212793600-212803200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:212793600-212810600	Weak transcription	Esophagus	oesophagus
9	chr1:212793800-212802400	Weak transcription	Gastric	stomach
10	chr1:212793800-212802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212793800-212803000	Weak transcription	Right Ventricle	heart
12	chr1:212793800-212803200	Weak transcription	Brain Anterior Caudate	brain
13	chr1:212794000-212801400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:212794000-212803200	Weak transcription	GM12878-XiMat	blood
15	chr1:212794200-212803200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:212794400-212801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:212794400-212803200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:212794400-212803600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:212794400-212812200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:212794600-212801400	Weak transcription	Fetal Intestine Large	intestine
21	chr1:212794600-212803200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:212794800-212803200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:212794800-212803200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:212795000-212801400	Weak transcription	Liver	Liver
25	chr1:212795200-212802800	Weak transcription	Placenta	Placenta
26	chr1:212795200-212803200	Weak transcription	Left Ventricle	heart
27	chr1:212799000-212803200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:212799400-212803600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:212800000-212803200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:212800800-212803800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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