Variant report

Variant	rs1369509
Chromosome Location	chr2:134183006-134183007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10165601	0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[TSI][hapmap]
rs10171473	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10175744	0.88[CHB][hapmap];0.91[TSI][hapmap]
rs10180047	0.88[CHB][hapmap];0.93[CHD][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs10182656	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10184630	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs10193087	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10193730	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10196395	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10204436	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10204527	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10206474	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11898252	0.86[ASN][1000 genomes]
rs12327930	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12328976	0.88[CHB][hapmap]
rs13392963	0.88[CHB][hapmap]
rs13396831	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13396930	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13406057	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs13406354	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs13407205	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13407503	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs13408835	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13411233	0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[TSI][hapmap]
rs13412956	0.88[CHB][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13421761	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13426157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs13426681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13432602	0.82[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap]
rs1346776	0.84[TSI][hapmap]
rs1369510	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs1430166	0.81[TSI][hapmap]
rs1430168	0.88[CHB][hapmap]
rs1435556	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1435563	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1435564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1435565	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1435566	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1561018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16824299	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16824301	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16824303	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16824511	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs16824573	0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17745593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17745851	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17802295	0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs1898008	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2115864	0.88[CHB][hapmap]
rs2164326	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35892150	0.87[EUR][1000 genomes]
rs4588241	0.88[CHB][hapmap]
rs55788182	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62177669	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177672	0.83[ASN][1000 genomes]
rs62180016	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7573164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9287426	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs990476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1369509	C2orf27B	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134171400-134183800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:134178200-134185200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:134178400-134183200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:134178600-134183600	Enhancers	Brain Substantia Nigra	brain
5	chr2:134178800-134183600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:134179000-134183200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:134181000-134183200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:134181000-134183600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:134181000-134186800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:134181000-134188200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:134181000-134188200	Weak transcription	HMEC	breast
12	chr2:134181000-134188800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:134181400-134184600	Weak transcription	Hela-S3	cervix
14	chr2:134181400-134191000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:134182200-134183200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:134182400-134183400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:134182400-134188400	Weak transcription	A549	lung
18	chr2:134182600-134183200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:134182600-134183200	Enhancers	Brain Germinal Matrix	brain
20	chr2:134182600-134183400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:134182600-134183400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr2:134182600-134188000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:134182800-134183200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:134182800-134186600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:134182800-134188400	Weak transcription	Osteobl	bone
26	chr2:134182800-134192600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:134183000-134184600	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:134183000-134189000	Weak transcription	NHDF-Ad	bronchial
29	chr2:134183000-134191000	Weak transcription	NH-A	brain

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