Variant report

Variant	rs412142
Chromosome Location	chr20:30183598-30183599
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:30156032..30163355-chr20:30174111..30184314,17	K562	blood:
2	chr20:30175191..30187262-chr20:30189260..30197267,31	K562	blood:
3	chr20:30135179..30137542-chr20:30180699..30183633,2	MCF-7	breast:
4	chr15:67813199..67813778-chr20:30183535..30184220,2	Hela-S3	cervix:
5	chr20:30153361..30167278-chr20:30173376..30187153,33	MCF-7	breast:
6	chr20:30175872..30185816-chr20:30189435..30197267,30	K562	blood:
7	chr11:10830086..10830659-chr20:30183352..30184054,2	Hela-S3	cervix:
8	chr20:30177624..30180444-chr20:30183202..30184783,2	MCF-7	breast:
9	chr20:30154561..30159420-chr20:30179648..30183966,5	MCF-7	breast:
10	chr20:30159490..30164990-chr20:30179028..30186560,14	MCF-7	breast:
11	chr20:30168108..30171242-chr20:30181982..30185058,3	MCF-7	breast:
12	chr20:30168057..30170840-chr20:30181174..30184292,3	K562	blood:
13	chr20:30183089..30184077-chr5:43483854..43484455,2	Hela-S3	cervix:
14	chr20:30183455..30183956-chr3:25937374..25937874,2	Hela-S3	cervix:
15	chr20:30169072..30171747-chr20:30182396..30185186,3	MCF-7	breast:
16	chr19:40502669..40503284-chr20:30183254..30184045,2	HCT-116	colon:
17	chr20:30182683..30185772-chr20:30199520..30202457,3	K562	blood:
18	chr20:30159399..30162478-chr20:30183127..30187352,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000201770	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000189227	Chromatin interaction
ENSG00000187187	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000259673	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000101294	Chromatin interaction
ENSG00000101898	Chromatin interaction
ENSG00000230613	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11699147	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1194993	0.99[ASN][1000 genomes]
rs1543438	0.83[JPT][hapmap]
rs2233832	0.90[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs3761199	0.83[JPT][hapmap]
rs3861819	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs73612002	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73613718	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
2	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
3	nsv1062612	chr20:29833958-30219337	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
4	nsv1061673	chr20:29833958-30649496	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
5	nsv544232	chr20:29833958-30649496	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
6	nsv1058344	chr20:29835037-30386611	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	402 gene(s)	inside rSNPs	diseases
7	nsv1059672	chr20:29835037-30621271	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
8	esv2763228	chr20:29835049-30239522	Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
9	nsv949085	chr20:29846303-30473188	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	414 gene(s)	inside rSNPs	diseases
10	nsv1058020	chr20:29877877-30197681	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
11	nsv544236	chr20:29877877-30197681	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
12	nsv1063560	chr20:29877877-30435888	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
13	nsv544237	chr20:29877877-30435888	Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
14	nsv458961	chr20:29893501-30275906	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
15	nsv585911	chr20:29893501-30275906	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
16	nsv1067177	chr20:29900572-30299363	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
17	nsv1057001	chr20:30108573-30190814	Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
18	nsv544239	chr20:30108573-30190814	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Active TSS 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	66 gene(s)	inside rSNPs	diseases
19	nsv1056783	chr20:30140632-30625189	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	400 gene(s)	inside rSNPs	diseases
20	nsv544240	chr20:30140632-30625189	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	400 gene(s)	inside rSNPs	diseases
21	nsv979478	chr20:30158946-30200763	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	363 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs412142	ID1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:30176200-30184000	Weak transcription	Ovary	ovary
2	chr20:30176400-30183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:30179400-30183600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr20:30180400-30183800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr20:30180400-30185400	Enhancers	Placenta	Placenta
6	chr20:30181000-30184000	Enhancers	Liver	Liver
7	chr20:30181000-30184400	Flanking Active TSS	HepG2	liver
8	chr20:30181000-30184800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:30181000-30185000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:30181000-30185400	Enhancers	Fetal Intestine Large	intestine
11	chr20:30181000-30185400	Enhancers	K562	blood
12	chr20:30181000-30186000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:30181200-30183600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr20:30181200-30184400	Enhancers	HUVEC	blood vessel
15	chr20:30181200-30185000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:30181200-30185200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr20:30181200-30185200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr20:30181200-30185200	Enhancers	NHDF-Ad	bronchial
19	chr20:30181200-30185200	Enhancers	NHLF	lung
20	chr20:30181400-30184200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr20:30181400-30184200	Enhancers	Esophagus	oesophagus
22	chr20:30181400-30184200	Enhancers	Right Ventricle	heart
23	chr20:30181400-30184200	Enhancers	HMEC	breast
24	chr20:30181400-30184400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:30181400-30184800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:30181400-30185000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr20:30181400-30185200	Enhancers	Fetal Intestine Small	intestine
28	chr20:30181400-30185400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:30181400-30185600	Enhancers	Adipose Nuclei	Adipose
30	chr20:30181600-30183600	Enhancers	Right Atrium	heart
31	chr20:30181600-30184200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr20:30181600-30184800	Enhancers	Fetal Muscle Trunk	muscle
33	chr20:30182000-30183800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr20:30182000-30185000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr20:30182200-30183800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr20:30182200-30184200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:30182200-30184200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr20:30182200-30184200	Enhancers	NH-A	brain
39	chr20:30182200-30184400	Flanking Active TSS	A549	lung
40	chr20:30182200-30185200	Enhancers	Gastric	stomach
41	chr20:30182200-30185400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr20:30182400-30183800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:30182400-30184200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr20:30182400-30184200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr20:30182400-30184800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:30182400-30185000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr20:30182400-30185000	Enhancers	Fetal Kidney	kidney
48	chr20:30182400-30185000	Enhancers	Fetal Lung	lung
49	chr20:30182400-30185200	Enhancers	Colonic Mucosa	Colon
50	chr20:30182600-30184200	Enhancers	Brain Cingulate Gyrus	brain

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