Variant report

Variant	rs12444462
Chromosome Location	chr16:74786461-74786462
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74785769..74787577-chr16:74789520..74792247,3	K562	blood:
2	chr16:74786372..74788961-chr16:74805816..74808724,2	MCF-7	breast:
3	chr16:74784525..74787559-chr16:74790634..74792634,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103089	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1024503	1.00[ASN][1000 genomes]
rs10514386	1.00[ASN][1000 genomes]
rs11645307	1.00[ASN][1000 genomes]
rs11863300	1.00[ASN][1000 genomes]
rs11864313	1.00[ASN][1000 genomes]
rs11864349	1.00[ASN][1000 genomes]
rs11866550	1.00[ASN][1000 genomes]
rs12444618	1.00[ASN][1000 genomes]
rs12445200	1.00[ASN][1000 genomes]
rs12446147	1.00[ASN][1000 genomes]
rs12447968	1.00[ASN][1000 genomes]
rs12919626	1.00[ASN][1000 genomes]
rs12921263	1.00[ASN][1000 genomes]
rs14308	1.00[ASN][1000 genomes]
rs28810133	1.00[ASN][1000 genomes]
rs34130324	1.00[ASN][1000 genomes]
rs34393456	1.00[ASN][1000 genomes]
rs34398985	1.00[ASN][1000 genomes]
rs34937987	1.00[ASN][1000 genomes]
rs34992867	1.00[ASN][1000 genomes]
rs35038783	1.00[ASN][1000 genomes]
rs35173843	1.00[ASN][1000 genomes]
rs35195349	1.00[ASN][1000 genomes]
rs35456018	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35937344	1.00[ASN][1000 genomes]
rs4887788	1.00[ASN][1000 genomes]
rs4888281	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888307	1.00[ASN][1000 genomes]
rs4985359	1.00[ASN][1000 genomes]
rs4985360	0.85[MEX][hapmap]
rs55836977	1.00[ASN][1000 genomes]
rs55859029	1.00[ASN][1000 genomes]
rs56009261	1.00[ASN][1000 genomes]
rs56313952	1.00[ASN][1000 genomes]
rs58303079	1.00[ASN][1000 genomes]
rs62052860	1.00[ASN][1000 genomes]
rs62052861	1.00[ASN][1000 genomes]
rs71392613	1.00[ASN][1000 genomes]
rs71392614	1.00[ASN][1000 genomes]
rs71392615	1.00[ASN][1000 genomes]
rs7203228	1.00[ASN][1000 genomes]
rs72794783	1.00[ASN][1000 genomes]
rs72796668	1.00[ASN][1000 genomes]
rs72796671	1.00[ASN][1000 genomes]
rs72796672	1.00[ASN][1000 genomes]
rs72796678	1.00[ASN][1000 genomes]
rs72796696	1.00[ASN][1000 genomes]
rs72798603	1.00[ASN][1000 genomes]
rs72798608	1.00[ASN][1000 genomes]
rs72798613	1.00[ASN][1000 genomes]
rs72798621	1.00[ASN][1000 genomes]
rs74024559	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74024565	1.00[ASN][1000 genomes]
rs8047659	1.00[ASN][1000 genomes]
rs8062012	1.00[ASN][1000 genomes]
rs933335	0.86[GIH][hapmap]
rs9937139	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
9	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12444462	HPR	cis	cerebellum	SCAN
rs12444462	MON1B	cis	cerebellum	SCAN
rs12444462	LDHD	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74777600-74802400	Weak transcription	Thymus	Thymus
2	chr16:74779600-74792800	Weak transcription	Pancreas	Pancrea
3	chr16:74779600-74803800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr16:74779600-74805400	Weak transcription	Colonic Mucosa	Colon
5	chr16:74780000-74805200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr16:74780200-74787400	Weak transcription	Stomach Mucosa	stomach
7	chr16:74780200-74802400	Weak transcription	Fetal Intestine Small	intestine
8	chr16:74782800-74789600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr16:74783800-74790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:74783800-74790000	Weak transcription	Gastric	stomach
11	chr16:74784000-74786800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr16:74784200-74787200	Weak transcription	Fetal Intestine Large	intestine
13	chr16:74784600-74788600	Weak transcription	Brain Angular Gyrus	brain
14	chr16:74784800-74786600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:74784800-74787000	Weak transcription	Brain Substantia Nigra	brain
16	chr16:74784800-74787800	Weak transcription	A549	lung
17	chr16:74784800-74790000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:74785000-74791200	Weak transcription	Brain Anterior Caudate	brain
19	chr16:74785800-74786800	Weak transcription	Brain Hippocampus Middle	brain

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