Variant report

Variant	rs5637
Chromosome Location	chr12:120762765-120762766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120727172..120733111-chr12:120749358..120767260,47	MCF-7	breast:
2	chr12:120761038..120763452-chr12:120881221..120883807,2	K562	blood:
3	chr12:120761708..120763403-chr12:120867083..120868587,2	MCF-7	breast:
4	chr12:120761819..120763866-chr12:120791381..120794631,4	K562	blood:
5	chr12:120758856..120760738-chr12:120761822..120763461,2	MCF-7	breast:
6	chr12:120762089..120763810-chr12:120905605..120907503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111786	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10849743	0.86[ASN][1000 genomes]
rs11065075	0.96[EUR][1000 genomes]
rs11065091	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11614028	0.81[EUR][1000 genomes]
rs1179387	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557769	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs206951	0.82[EUR][1000 genomes]
rs206966	0.85[CEU][hapmap]
rs2522129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522138	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522141	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2696027	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742038	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap]
rs67706074	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7137625	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7314115	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73416934	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs965791	0.92[CEU][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
3	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
5	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5637	GCN1L1	cis	multi-tissue	Pritchard
rs5637	MYLPF	trans	parietal	SCAN
rs5637	SIRT4	cis	parietal	SCAN
rs5637	OASL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120755400-120762800	Weak transcription	Gastric	stomach
2	chr12:120755400-120763200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:120755400-120763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:120756000-120763200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:120756200-120763200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:120756200-120763200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:120756200-120763200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:120756200-120763200	Weak transcription	GM12878-XiMat	blood
9	chr12:120756200-120763400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:120757000-120763200	Weak transcription	Thymus	Thymus
11	chr12:120759400-120763200	Weak transcription	K562	blood
12	chr12:120760000-120763400	Weak transcription	Fetal Kidney	kidney
13	chr12:120760200-120763200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:120760200-120763200	Weak transcription	Stomach Mucosa	stomach
15	chr12:120760200-120763400	Weak transcription	Colonic Mucosa	Colon
16	chr12:120760400-120762800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:120760400-120763400	Weak transcription	A549	lung
18	chr12:120760600-120763200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:120761200-120765800	Active TSS	Pancreas	Pancrea
20	chr12:120761400-120765600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:120761800-120763600	Weak transcription	Spleen	Spleen
22	chr12:120762400-120763200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:120762400-120763400	Enhancers	Liver	Liver
24	chr12:120762400-120763400	Enhancers	Fetal Intestine Small	intestine
25	chr12:120762600-120762800	Enhancers	HepG2	liver
26	chr12:120762600-120763400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:120762600-120763400	Enhancers	Fetal Intestine Large	intestine

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