Variant report

Variant	rs3862905
Chromosome Location	chr1:76763785-76763786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10218683	0.84[CEU][hapmap]
rs11162104	0.84[CEU][hapmap]
rs11162113	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162116	0.98[ASN][1000 genomes]
rs12028135	0.84[CEU][hapmap]
rs12036155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1414486	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1537782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3908823	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56831847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	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
rs3862905	ELTD1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76755800-76783000	Weak transcription	Fetal Lung	lung
2	chr1:76756600-76764200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:76756600-76764400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:76756800-76763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:76757200-76764200	Weak transcription	Fetal Thymus	thymus
6	chr1:76757200-76764400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:76759800-76766600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:76760400-76779200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:76760800-76764600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:76761000-76766200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:76761200-76763800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:76761200-76764000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:76761200-76768200	Enhancers	Primary T cells from cord blood	blood
14	chr1:76761400-76765200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:76761600-76764000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:76762000-76764200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:76762200-76764000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:76762200-76764000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:76762400-76763800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:76762400-76763800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:76762400-76763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:76762400-76764200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:76762400-76764200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:76762400-76764200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:76762600-76763800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:76762800-76764000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:76763200-76767600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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