Variant report

Variant	rs16876587
Chromosome Location	chr6:35435340-35435341
allele	C/T
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	CTCF	chr6:35435300-35435450	GM12873	blood:	n/a	chr6:35435348-35435361
2	POLR2A	chr6:35435014-35442921	PFSK-1	brain:	n/a	n/a
3	NR2F2	chr6:35435137-35437122	K562	blood:	n/a	n/a
4	POLR2A	chr6:35435158-35444051	Hela-S3	cervix:	n/a	n/a
5	PML	chr6:35435243-35436795	K562	blood:	n/a	chr6:35436062-35436070
6	CBX3	chr6:35435229-35436888	K562	blood:	n/a	n/a
7	GATA3	chr6:35435322-35436552	MCF-7	breast:	n/a	chr6:35435401-35435410 chr6:35435398-35435407
8	JUND	chr6:35435314-35436439	K562	blood:	n/a	chr6:35435400-35435408 chr6:35435399-35435409 chr6:35435398-35435410 chr6:35435399-35435409 chr6:35435399-35435409 chr6:35435401-35435412 chr6:35435399-35435409
9	POLR2A	chr6:35435238-35443013	K562	blood:	n/a	n/a
10	POLR2A	chr6:35435032-35444467	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr6:35435186-35445490	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:35435152-35443652	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr6:35435112-35438458	K562	blood:	n/a	n/a
14	POLR2A	chr6:35435090-35438453	K562	blood:	n/a	n/a
15	POLR2A	chr6:35435279-35442556	K562	blood:	n/a	n/a
16	POLR2A	chr6:35435133-35443012	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr6:35435191-35443072	K562	blood:	n/a	n/a
18	CTCF	chr6:35435330-35436816	SK-N-SH	brain:	n/a	chr6:35436045-35436061 chr6:35435948-35435961 chr6:35435348-35435361 chr6:35436044-35436062
19	POLR2A	chr6:35435273-35441510	HepG2	liver:	n/a	n/a
20	PML	chr6:35435316-35438141	GM12878	blood:	n/a	chr6:35436062-35436070
21	MYBL2	chr6:35435331-35436827	HepG2	liver:	n/a	n/a
22	HCFC1	chr6:35435211-35437279	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr6:35435090-35444246	K562	blood:	n/a	n/a
24	POLR2A	chr6:35435237-35443815	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr6:35435310-35444078	K562	blood:	n/a	n/a
26	POLR2A	chr6:35435177-35444394	K562	blood:	n/a	n/a
27	MTA3	chr6:35435282-35437925	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:35226066..35229330-chr6:35434346..35438215,4	K562	blood:
2	chr6:35308405..35313609-chr6:35434054..35440248,12	K562	blood:
3	chr6:35410187..35412214-chr6:35434908..35436495,2	K562	blood:
4	chr6:35260730..35269335-chr6:35433870..35444063,22	MCF-7	breast:
5	chr6:35434857..35438603-chr6:35692996..35696802,4	K562	blood:
6	chr6:35270811..35278072-chr6:35434777..35439344,8	MCF-7	breast:
7	chr6:35308378..35313609-chr6:35433550..35439145,12	K562	blood:
8	chr6:35309215..35314259-chr6:35432456..35439068,10	MCF-7	breast:
9	chr6:35227094..35229802-chr6:35433183..35436613,4	K562	blood:
10	chr6:35435012..35436668-chr6:35752247..35755003,2	MCF-7	breast:
11	chr11:2397606..2400001-chr6:35434655..35437647,2	K562	blood:
12	chr6:35434775..35437842-chr6:35701549..35705876,5	MCF-7	breast:
13	chr6:35418617..35424875-chr6:35434196..35438070,12	MCF-7	breast:
14	chr6:35226330..35228825-chr6:35434969..35437843,3	MCF-7	breast:
15	chr6:35257372..35267692-chr6:35433856..35438688,25	K562	blood:
16	chr6:35415818..35424678-chr6:35432486..35440672,36	K562	blood:
17	chr6:35433822..35437754-chr6:35703135..35706478,6	K562	blood:
18	chr6:35257372..35267871-chr6:35433266..35439192,25	K562	blood:

Variant related genes	Relation type
RPL10A	TF binding region
ENSG00000023892	Chromatin interaction
ENSG00000204140	Chromatin interaction
ENSG00000227154	Chromatin interaction
ENSG00000157343	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000096060	Chromatin interaction
ENSG00000065029	Chromatin interaction
ENSG00000232909	Chromatin interaction
ENSG00000238184	Chromatin interaction
ENSG00000112033	Chromatin interaction
ENSG00000110651	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11553979	1.00[ASN][1000 genomes]
rs11962317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876584	1.00[ASN][1000 genomes]
rs3800376	1.00[ASN][1000 genomes]
rs41271261	1.00[ASN][1000 genomes]
rs45479891	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457822	0.95[ASN][1000 genomes]
rs6457823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457824	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6927202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7768070	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462087	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462089	0.98[ASN][1000 genomes]
rs9470027	0.95[ASN][1000 genomes]
rs9470030	0.95[ASN][1000 genomes]
rs9470033	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470038	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
3	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
4	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
6	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
7	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35421000-35435400	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:35421200-35435400	Weak transcription	Brain Anterior Caudate	brain
3	chr6:35421400-35435400	Weak transcription	Colonic Mucosa	Colon
4	chr6:35421400-35435400	Weak transcription	Fetal Kidney	kidney
5	chr6:35421400-35435400	Weak transcription	Pancreas	Pancrea
6	chr6:35421600-35435400	Weak transcription	A549	lung
7	chr6:35421600-35435400	Weak transcription	NH-A	brain
8	chr6:35422200-35435400	Weak transcription	Small Intestine	intestine
9	chr6:35422600-35435400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:35422800-35435400	Weak transcription	Fetal Brain Male	brain
11	chr6:35422800-35435600	Weak transcription	Right Atrium	heart
12	chr6:35423000-35435400	Weak transcription	NHDF-Ad	bronchial
13	chr6:35423400-35435400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:35424000-35435600	Weak transcription	Psoas Muscle	Psoas
15	chr6:35424200-35435400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:35426600-35435400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:35427400-35435400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:35427600-35435400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:35427600-35435400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:35427600-35435400	Weak transcription	Left Ventricle	heart
21	chr6:35427600-35435400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:35427800-35435400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:35427800-35435400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:35427800-35435400	Weak transcription	Osteobl	bone
25	chr6:35428000-35435400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:35428000-35435400	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:35428000-35435600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:35428000-35435600	Weak transcription	Gastric	stomach
29	chr6:35428600-35435400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:35428600-35435400	Weak transcription	Thymus	Thymus
31	chr6:35428600-35435600	Weak transcription	Right Ventricle	heart
32	chr6:35428600-35435600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:35429000-35435400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:35429200-35435400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:35429400-35435400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:35430400-35435800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:35430800-35435600	Weak transcription	HSMM	muscle
38	chr6:35430800-35435800	Weak transcription	Lung	lung
39	chr6:35431000-35435600	Weak transcription	Aorta	Aorta
40	chr6:35431400-35435400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:35431400-35435400	Weak transcription	Liver	Liver
42	chr6:35431400-35435400	Weak transcription	Fetal Lung	lung
43	chr6:35431800-35435400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:35431800-35435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:35432000-35435400	Weak transcription	Adipose Nuclei	Adipose
46	chr6:35432000-35435600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:35432600-35435400	Strong transcription	HMEC	breast
48	chr6:35433200-35435400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:35434000-35435400	Strong transcription	Fetal Brain Female	brain
50	chr6:35434200-35435400	Weak transcription	HUVEC	blood vessel

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