Variant report

Variant	rs557252
Chromosome Location	chr1:212680414-212680415
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12131037	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs12135668	0.89[EUR][1000 genomes]
rs12141407	0.89[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12729438	0.91[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs12741983	0.82[ASN][1000 genomes]
rs12753186	0.82[EUR][1000 genomes]
rs12754528	0.82[EUR][1000 genomes]
rs13374785	0.95[EUR][1000 genomes]
rs2292479	0.82[EUR][1000 genomes]
rs2292481	0.82[EUR][1000 genomes]
rs2292482	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs3001262	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34543166	0.96[EUR][1000 genomes]
rs36056520	0.96[EUR][1000 genomes]
rs3951316	0.82[EUR][1000 genomes]
rs525176	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs572235	0.82[ASN][1000 genomes]
rs590156	0.81[ASN][1000 genomes]
rs591176	0.88[EUR][1000 genomes]
rs624387	0.99[EUR][1000 genomes]
rs626178	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs638527	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs653006	0.99[EUR][1000 genomes]
rs653532	0.99[EUR][1000 genomes]
rs6540742	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs6540743	0.82[ASN][1000 genomes]
rs6669813	0.87[EUR][1000 genomes]
rs6694514	0.81[ASN][1000 genomes]
rs6704297	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs679840	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs748517	0.89[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs7513550	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs7515863	0.82[ASN][1000 genomes]
rs7517259	0.82[EUR][1000 genomes]
rs7519767	0.82[EUR][1000 genomes]
rs7529867	0.87[EUR][1000 genomes]
rs7537826	0.82[ASN][1000 genomes]
rs7553229	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs796930	0.98[EUR][1000 genomes]
rs806539	0.95[EUR][1000 genomes]
rs9430096	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs557252	TMEM206	cis	cerebellum	SCAN
rs557252	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs557252	TMEM206	cis	parietal	SCAN
rs557252	RPS6KC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212667200-212686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:212672200-212680600	Weak transcription	Right Atrium	heart
3	chr1:212675800-212680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:212679200-212681600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:212679600-212680600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:212679600-212681000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:212679600-212681000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:212679600-212681200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:212679600-212681400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:212679800-212680800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:212679800-212681000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:212679800-212681000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:212679800-212681200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:212680000-212680600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:212680000-212680800	Enhancers	Brain Anterior Caudate	brain
16	chr1:212680000-212681000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:212680000-212681000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:212680000-212681000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:212680000-212681000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:212680000-212681000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:212680000-212681000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:212680000-212681200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr1:212680000-212681200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:212680000-212681400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212680000-212681400	Enhancers	Brain Angular Gyrus	brain
26	chr1:212680000-212681400	Enhancers	Brain Hippocampus Middle	brain
27	chr1:212680200-212680600	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:212680200-212680800	Enhancers	Brain Substantia Nigra	brain
29	chr1:212680200-212681200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:212680200-212681200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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