Variant report

Variant	rs2839670
Chromosome Location	chr10:26504340-26504341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr10:26503915-26507739	H1-neurons	neurons:	n/a	n/a
2	CTBP2	chr10:26503474-26507402	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr10:26502119-26508104	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr10:26503373-26508237	H1-neurons	neurons:	n/a	n/a
5	REST	chr10:26503452-26505889	H1-neurons	neurons:	n/a	chr10:26505231-26505240 chr10:26505220-26505240 chr10:26503893-26503900 chr10:26505220-26505240 chr10:26505195-26505208 chr10:26505220-26505234 chr10:26505222-26505232 chr10:26505227-26505240 chr10:26505224-26505237 chr10:26505220-26505240 chr10:26505221-26505239 chr10:26505224-26505237
6	SUZ12	chr10:26503603-26508046	NT2-D1	testis:	n/a	n/a
7	TAF1	chr10:26503419-26505793	H1-neurons	neurons:	n/a	n/a
8	ELF1	chr10:26504252-26504665	GM12878	blood:	n/a	chr10:26504419-26504430 chr10:26504420-26504429 chr10:26504622-26504631 chr10:26504419-26504428
9	REST	chr10:26501382-26511273	H1-neurons	neurons:	n/a	chr10:26506086-26506100 chr10:26505231-26505240 chr10:26505220-26505240 chr10:26503893-26503900 chr10:26505220-26505240 chr10:26506967-26506980 chr10:26508383-26508401 chr10:26505195-26505208 chr10:26505220-26505234 chr10:26507108-26507121 chr10:26505222-26505232 chr10:26505227-26505240 chr10:26505224-26505237 chr10:26505220-26505240 chr10:26505221-26505239 chr10:26505224-26505237 chr10:26502538-26502551
10	SIN3A	chr10:26502684-26506045	H1-hESC	embryonic stem cell:	n/a	chr10:26505222-26505231 chr10:26505431-26505444 chr10:26503916-26503926 chr10:26505045-26505054 chr10:26505221-26505235 chr10:26505227-26505240

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABI1-10	chr10:26501467-26505235	NONHSAT011822

Variant related genes	Relation type
GAD2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508715	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014993	0.90[CHB][hapmap]
rs11014995	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014996	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11819063	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12243037	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1330572	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1330581	0.81[JPT][hapmap]
rs2236417	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236418	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839669	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781108	0.89[TSI][hapmap]
rs3781113	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4144102	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4749108	0.89[TSI][hapmap]
rs61839365	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7071922	0.84[ASN][1000 genomes]
rs7072136	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073982	0.91[JPT][hapmap]
rs7076544	0.84[CHB][hapmap]
rs8190582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190598	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8190647	0.94[CHB][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8190706	0.80[CEU][hapmap]
rs8190754	0.89[TSI][hapmap]
rs8190809	0.82[CHB][hapmap]
rs994502	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2839670	COMMD3	cis	parietal	SCAN
rs2839670	ABI1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26502600-26505000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
2	chr10:26502600-26505200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr10:26502800-26508600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:26503000-26507800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr10:26503200-26505400	Active TSS	Brain Germinal Matrix	brain
6	chr10:26503400-26504400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr10:26503400-26504400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:26503400-26504600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
9	chr10:26503400-26504600	Bivalent/Poised TSS	Fetal Brain Female	brain
10	chr10:26503400-26505000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr10:26503600-26504400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
12	chr10:26503600-26504400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr10:26503600-26505000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:26503600-26505200	Enhancers	Pancreas	Pancrea
15	chr10:26503600-26505800	Flanking Bivalent TSS/Enh	Dnd41	blood
16	chr10:26503600-26506600	Bivalent Enhancer	Fetal Thymus	thymus
17	chr10:26503600-26507400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr10:26503600-26507600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr10:26503600-26507600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr10:26503800-26504800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:26503800-26505800	Enhancers	Gastric	stomach
22	chr10:26503800-26506000	Bivalent Enhancer	Spleen	Spleen
23	chr10:26503800-26506200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:26503800-26507200	Bivalent Enhancer	Liver	Liver
25	chr10:26503800-26507200	Bivalent Enhancer	Fetal Brain Male	brain
26	chr10:26503800-26507600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr10:26504000-26504400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
28	chr10:26504000-26504400	Bivalent Enhancer	Colonic Mucosa	Colon
29	chr10:26504000-26504600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr10:26504000-26504600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr10:26504000-26504600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr10:26504000-26504800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr10:26504000-26505000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr10:26504000-26505200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
35	chr10:26504000-26505200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
36	chr10:26504000-26505600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:26504000-26505800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:26504000-26505800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:26504000-26506000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr10:26504000-26507200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr10:26504200-26504400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr10:26504200-26504400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr10:26504200-26504400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:26504200-26504400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:26504200-26504400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
46	chr10:26504200-26504400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr10:26504200-26504400	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr10:26504200-26504400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:26504200-26504400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr10:26504200-26504400	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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