Variant report

Variant	rs2839668
Chromosome Location	chr10:26503114-26503115
allele	A/G
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	POLR2A	chr10:26502709-26503365	H1-neurons	neurons:	n/a	n/a
2	SP1	chr10:26502895-26503415	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr10:26502811-26503233	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr10:26502974-26503358	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTBP2	chr10:26502331-26503263	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr10:26502119-26508104	H1-neurons	neurons:	n/a	n/a
7	NANOG	chr10:26502967-26503420	H1-hESC	embryonic stem cell:	n/a	n/a
8	NANOG	chr10:26502850-26503327	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUND	chr10:26502996-26503541	H1-hESC	embryonic stem cell:	n/a	chr10:26503176-26503185 chr10:26503126-26503140
10	BACH1	chr10:26503004-26503986	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF143	chr10:26502865-26503178	H1-hESC	embryonic stem cell:	n/a	n/a
12	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
13	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: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11014982	0.88[EUR][1000 genomes]
rs12243085	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12263667	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12267286	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1556234	0.95[AMR][1000 genomes]
rs2298124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839674	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839676	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839677	0.95[AMR][1000 genomes]
rs33947968	0.85[EUR][1000 genomes]
rs3781105	0.95[AMR][1000 genomes]
rs3781110	0.95[AMR][1000 genomes]
rs3781116	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3904297	0.80[EUR][1000 genomes]
rs3904298	0.80[EUR][1000 genomes]
rs4121076	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41304609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56296397	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56981377	0.86[EUR][1000 genomes]
rs59122563	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59914979	0.80[EUR][1000 genomes]
rs6482538	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482539	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482540	0.80[EUR][1000 genomes]
rs7067786	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73594327	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7908975	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8190597	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190635	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8190639	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8190641	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8190646	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8190649	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8190650	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8190718	0.95[AMR][1000 genomes]
rs8190750	0.95[AMR][1000 genomes]
rs8190770	0.95[AMR][1000 genomes]
rs8190775	0.95[AMR][1000 genomes]
rs8190787	0.95[AMR][1000 genomes]
rs8190789	0.95[AMR][1000 genomes]
rs8190800	0.95[AMR][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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26501000-26503800	Weak transcription	Gastric	stomach
2	chr10:26501400-26503200	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr10:26502000-26504200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:26502600-26503400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:26502600-26505000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr10:26502600-26505200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr10:26502800-26503600	Bivalent Enhancer	Dnd41	blood
8	chr10:26502800-26508600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr10:26503000-26503400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr10:26503000-26503400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr10:26503000-26503400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr10:26503000-26503400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr10:26503000-26503400	Bivalent Enhancer	Fetal Brain Female	brain
14	chr10:26503000-26503600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:26503000-26503600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr10:26503000-26507800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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