Variant report

Variant	rs9931439
Chromosome Location	chr16:74846932-74846933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:74808159..74809197-chr16:74846688..74848115,4	K562	blood:
2	chr16:74846723..74847755-chr16:74896368..74897323,9	K562	blood:
3	chr16:74846665..74847640-chr16:74896133..74897263,15	MCF-7	breast:
4	chr16:74701971..74704127-chr16:74845160..74847638,2	MCF-7	breast:
5	chr16:74743004..74743985-chr16:74846664..74847648,5	K562	blood:
6	chr16:74846819..74847580-chr16:74875766..74876759,2	K562	blood:
7	chr16:74743044..74744187-chr16:74846300..74847985,46	MCF-7	breast:
8	chr16:74733905..74734725-chr16:74846845..74847676,2	MCF-7	breast:
9	chr16:74742777..74743959-chr16:74846396..74847939,16	MCF-7	breast:
10	chr16:74846710..74847551-chr16:75232890..75233892,3	K562	blood:
11	chr16:74846668..74847725-chr16:74896168..74897246,10	MCF-7	breast:
12	chr16:74846696..74847406-chr16:74895112..74895797,2	MCF-7	breast:
13	chr16:74780872..74781750-chr16:74846558..74847234,2	MCF-7	breast:
14	chr16:74846831..74847572-chr16:74877008..74877733,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168404	Chromatin interaction
ENSG00000103089	Chromatin interaction
ENSG00000263661	Chromatin interaction
ENSG00000261458	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11864552	0.81[ASN][1000 genomes]
rs12102427	0.94[ASN][1000 genomes]
rs1557906	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1820251	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28480147	0.94[ASN][1000 genomes]
rs28765991	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28811995	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888283	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4888284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6564168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67209233	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7185246	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7188641	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7194123	0.81[ASN][1000 genomes]
rs73618323	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8048578	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8055156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060979	1.00[JPT][hapmap]
rs929881	1.00[JPT][hapmap]
rs933334	1.00[JPT][hapmap]
rs933335	1.00[JPT][hapmap]
rs9923923	0.94[ASN][1000 genomes]
rs9931664	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
7	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
8	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
9	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
10	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
11	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
12	esv2761913	chr16:74828988-74876348	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv431516	chr16:74840166-75099566	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9931439	RFWD3	cis	parietal	SCAN
rs9931439	CALB2	cis	parietal	SCAN
rs9931439	WWP2	cis	parietal	SCAN
rs9931439	LDHD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74844400-74847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:74844600-74847600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr16:74845400-74847000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr16:74845600-74847600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr16:74846000-74847400	Enhancers	Brain Substantia Nigra	brain
6	chr16:74846000-74847600	Enhancers	Brain Angular Gyrus	brain
7	chr16:74846000-74847600	Enhancers	Brain Hippocampus Middle	brain
8	chr16:74846000-74848000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:74846200-74847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr16:74846200-74847200	Weak transcription	Lung	lung
11	chr16:74846200-74847400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:74846200-74847600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr16:74846200-74847600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr16:74846200-74848000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr16:74846200-74857400	Weak transcription	Gastric	stomach
16	chr16:74846400-74847400	Weak transcription	Right Atrium	heart
17	chr16:74846400-74847600	Enhancers	Stomach Mucosa	stomach
18	chr16:74846400-74851000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:74846600-74847000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:74846600-74847000	Weak transcription	Brain Anterior Caudate	brain
21	chr16:74846600-74847000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr16:74846600-74847000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr16:74846600-74847000	Weak transcription	Hela-S3	cervix
24	chr16:74846800-74847000	Enhancers	HepG2	liver
25	chr16:74846800-74847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:74846800-74847400	Enhancers	Fetal Thymus	thymus
27	chr16:74846800-74847600	Enhancers	Fetal Intestine Small	intestine

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