Variant report

Variant	rs71631461
Chromosome Location	chr20:30166101-30166102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:30164651-30166180	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr20:30163897-30166627	HepG2	liver:	n/a	n/a
3	SP1	chr20:30165718-30166139	HepG2	liver:	n/a	n/a
4	SP1	chr20:30165718-30166130	A549	lung:	n/a	n/a
5	SP1	chr20:30165587-30166310	H1-hESC	embryonic stem cell:	n/a	n/a
6	NFYA	chr20:30165770-30166193	K562	blood:	n/a	chr20:30165916-30165934 chr20:30165892-30165910 chr20:30165941-30165959
7	CHD2	chr20:30165780-30166138	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr20:30165759-30166140	GM12878	blood:	n/a	n/a
9	SP1	chr20:30165652-30166177	A549	lung:	n/a	n/a
10	CBX3	chr20:30165616-30166135	K562	blood:	n/a	n/a
11	NFYB	chr20:30165713-30166252	GM12878	blood:	n/a	chr20:30165947-30165962 chr20:30165922-30165937
12	NFYA	chr20:30165778-30166155	Hela-S3	cervix:	n/a	chr20:30165916-30165934 chr20:30165892-30165910 chr20:30165941-30165959
13	SP1	chr20:30165711-30166164	K562	blood:	n/a	n/a
14	RAD21	chr20:30166071-30166652	H1-hESC	embryonic stem cell:	n/a	n/a
15	SP1	chr20:30165650-30166278	H1-hESC	embryonic stem cell:	n/a	n/a
16	NFYB	chr20:30165629-30166250	Hela-S3	cervix:	n/a	chr20:30165947-30165962 chr20:30165922-30165937
17	NFYB	chr20:30165700-30166251	K562	blood:	n/a	chr20:30165947-30165962 chr20:30165922-30165937

No.	Distal block	Cell Line	Cell type
1	chr20:30164316..30166609-chr20:30194699..30196653,2	K562	blood:
2	chr20:30164072..30166658-chr20:30166671..30168464,2	MCF-7	breast:
3	chr20:30141940..30170495-chr20:30187994..30206228,231	MCF-7	breast:
4	chr20:30165118..30167240-chr20:30307090..30309210,2	MCF-7	breast:
5	chr20:30164512..30167066-chr20:30299344..30301224,2	K562	blood:
6	chr20:30143968..30170533-chr20:30187214..30202891,198	MCF-7	breast:
7	chr20:30164343..30166998-chr20:30169602..30171995,2	MCF-7	breast:
8	chr20:30160926..30163666-chr20:30165718..30168864,4	MCF-7	breast:

Variant related genes	Relation type
RNU6-384P	TF binding region
ENSG00000264395	Chromatin interaction
ENSG00000230613	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000268457	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13154127	0.96[EUR][1000 genomes]
rs13154421	0.80[AMR][1000 genomes]
rs13165145	0.96[EUR][1000 genomes]
rs13174803	0.80[AMR][1000 genomes]
rs13182255	0.95[EUR][1000 genomes]
rs13185634	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13189140	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17192300	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17192503	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17800685	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1962207	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34107321	0.96[EUR][1000 genomes]
rs34205014	0.92[EUR][1000 genomes]
rs34434894	0.93[EUR][1000 genomes]
rs34573392	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34836131	0.95[EUR][1000 genomes]
rs34982640	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35005767	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35220247	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35290633	0.96[EUR][1000 genomes]
rs35319490	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35647517	0.80[AMR][1000 genomes]
rs35703604	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35831659	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35971576	0.92[EUR][1000 genomes]
rs3860733	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6893317	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71631455	0.96[EUR][1000 genomes]
rs71631457	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71631459	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71631463	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71631464	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71631467	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7709512	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv3345	chr20:30136856-30181749	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:30161600-30175200	Weak transcription	Lung	lung
2	chr20:30161800-30169400	Weak transcription	Right Atrium	heart
3	chr20:30161800-30175200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:30161800-30175200	Weak transcription	Fetal Kidney	kidney
5	chr20:30161800-30175200	Weak transcription	Pancreas	Pancrea
6	chr20:30162000-30168400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:30162000-30174200	Weak transcription	Fetal Muscle Leg	muscle
8	chr20:30162000-30175200	Weak transcription	Adipose Nuclei	Adipose
9	chr20:30162000-30175200	Weak transcription	Spleen	Spleen
10	chr20:30162200-30173400	Weak transcription	A549	lung
11	chr20:30162200-30175200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:30162200-30175200	Weak transcription	Fetal Lung	lung
13	chr20:30162800-30166600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr20:30162800-30167000	Weak transcription	HepG2	liver
15	chr20:30163000-30174800	Weak transcription	Placenta	Placenta
16	chr20:30163200-30175000	Weak transcription	Hela-S3	cervix
17	chr20:30164000-30167000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:30164800-30166400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr20:30165000-30168400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr20:30165000-30168400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:30165200-30167000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr20:30165200-30168400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr20:30165400-30168200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr20:30165400-30175000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:30165600-30166600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr20:30165600-30166800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr20:30165600-30168600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr20:30165800-30166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr20:30165800-30166200	ZNF genes & repeats	K562	blood
30	chr20:30165800-30166800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr20:30166000-30168400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr20:30166000-30174800	Weak transcription	Fetal Intestine Small	intestine

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