Variant report

Variant	rs56656810
Chromosome Location	chr16:30788759-30788760
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr16:30788148-30788784	K562	blood:	n/a	n/a
2	POLR2A	chr16:30788561-30788880	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:30788482-30788891	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:30787767-30792226	K562	blood:	n/a	n/a
5	POLR2A	chr16:30788535-30789383	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr16:30788032-30789703	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:30788586-30791156	HCT-116	colon:	n/a	n/a
8	POLR2A	chr16:30785774-30792079	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr16:30787921-30789650	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr16:30785553-30792383	K562	blood:	n/a	n/a
11	POLR2A	chr16:30782383-30800309	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:30787963-30789757	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr16:30788346-30790724	U87	brain:	n/a	n/a
14	POLR2A	chr16:30788158-30790879	HepG2	liver:	n/a	n/a
15	POLR2A	chr16:30788013-30790558	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr16:30787773-30789652	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr16:30788001-30792932	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:30786429-30791257	MCF10A-Er-Src	breast:	n/a	n/a
19	ELF1	chr16:30788501-30789041	A549	lung:	n/a	n/a
20	HEY1	chr16:30787911-30788954	K562	blood:	n/a	n/a
21	POLR2A	chr16:30788082-30789521	HepG2	liver:	n/a	n/a
22	MTA3	chr16:30787925-30788861	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:30785480-30792632	SK-N-MC	brain:	n/a	n/a
24	MBD4	chr16:30787976-30790178	HepG2	liver:	n/a	n/a
25	POLR2A	chr16:30782939-30789605	GM12878	blood:	n/a	n/a
26	SMC3	chr16:30788746-30788774	K562	blood:	n/a	n/a
27	POLR2A	chr16:30788068-30790778	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:30788557-30792372	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr16:30788630-30789653	GM12891	blood:	n/a	n/a
30	POLR2A	chr16:30788085-30791665	MCF-7	breast:	n/a	n/a
31	POLR2A	chr16:30788485-30788914	A549	lung:	n/a	n/a
32	POLR2A	chr16:30788573-30789014	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr16:30787875-30791713	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr16:30788057-30789436	K562	blood:	n/a	n/a
35	POLR2A	chr16:30788088-30792671	HepG2	liver:	n/a	n/a
36	BCL3	chr16:30788077-30789446	A549	lung:	n/a	chr16:30788454-30788461
37	HEY1	chr16:30788666-30789009	K562	blood:	n/a	n/a
38	POLR2A	chr16:30788593-30788845	ProgFib	skin:	n/a	n/a
39	POLR2A	chr16:30786103-30789729	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr16:30786496-30791679	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr16:30788461-30790474	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr16:30788010-30792654	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr16:30787933-30790525	K562	blood:	n/a	n/a
44	POLR2A	chr16:30787929-30788767	K562	blood:	n/a	n/a
45	POLR2A	chr16:30785842-30791670	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr16:30787892-30791715	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr16:30788532-30790288	U87	brain:	n/a	n/a
48	POLR2A	chr16:30788038-30788954	HCT-116	colon:	n/a	n/a
49	POLR2A	chr16:30787921-30788815	GM12892	blood:	n/a	n/a
50	POLR2A	chr16:30788014-30792667	K562	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30750130..30751710-chr16:30786597..30789576,2	K562	blood:
2	chr16:30787031..30789768-chr16:30814722..30816994,3	K562	blood:
3	chr16:30672949..30675838-chr16:30787007..30788848,2	K562	blood:
4	chr16:30787386..30789402-chr16:30849116..30851160,2	MCF-7	breast:
5	chr16:30785755..30789519-chr16:30993933..30997614,3	K562	blood:
6	chr16:30786009..30790115-chr16:30903648..30907620,6	MCF-7	breast:
7	chr16:30787481..30790193-chr16:30968511..30970450,2	K562	blood:
8	chr16:30785759..30789223-chr16:30822658..30825886,4	K562	blood:
9	chr16:30787481..30790093-chr16:30968266..30970450,2	K562	blood:
10	chr16:30369515..30371729-chr16:30786723..30788933,2	MCF-7	breast:
11	chr16:30785822..30789729-chr16:30809078..30811832,3	K562	blood:
12	chr16:30786387..30788885-chr16:30817095..30819249,4	K562	blood:
13	chr16:30783772..30791593-chr16:30931071..30936822,9	MCF-7	breast:
14	chr16:30786822..30789085-chr16:30886328..30888758,2	MCF-7	breast:
15	chr16:30785189..30790485-chr16:30931540..30936077,12	K562	blood:
16	chr16:30726174..30728075-chr16:30787184..30789746,3	K562	blood:
17	chr16:30405512..30407718-chr16:30786792..30789552,2	MCF-7	breast:
18	chr16:30784974..30791554-chr16:30930641..30936449,8	MCF-7	breast:
19	chr16:30749452..30756542-chr16:30785692..30792123,12	MCF-7	breast:
20	chr16:30707557..30712450-chr16:30785751..30791890,10	K562	blood:
21	chr16:30707849..30711301-chr16:30785397..30790684,8	K562	blood:
22	chr16:30785189..30790485-chr16:30931540..30935208,7	K562	blood:
23	chr16:30787489..30791955-chr16:30902887..30909666,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000262026	TF binding region
ENSG00000150281	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000260852	Chromatin interaction
ENSG00000260899	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000099385	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000211591	Chromatin interaction
ENSG00000262721	Chromatin interaction
ENSG00000260083	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000099364	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12447534	0.96[ASN][1000 genomes]
rs13337900	0.81[ASN][1000 genomes]
rs28853644	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34480360	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747486	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812999	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4889489	0.93[ASN][1000 genomes]
rs4889490	0.81[ASN][1000 genomes]
rs62057223	0.90[ASN][1000 genomes]
rs72799316	0.81[ASN][1000 genomes]
rs73524556	0.81[ASN][1000 genomes]
rs8050330	0.81[ASN][1000 genomes]
rs8058961	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9921835	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9933875	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh 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	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
11	nsv9438	chr16:30770203-30799442	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv905732	chr16:30788182-30837210	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30786600-30788800	Active TSS	Rectal Smooth Muscle	rectum
2	chr16:30787000-30788800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:30787400-30788800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr16:30787400-30790400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr16:30787600-30789000	Enhancers	Gastric	stomach
6	chr16:30787600-30789200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:30787600-30789400	Enhancers	Stomach Mucosa	stomach
8	chr16:30787600-30793000	Weak transcription	Esophagus	oesophagus
9	chr16:30787600-30793400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:30787600-30797600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr16:30787800-30788800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:30787800-30788800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr16:30787800-30788800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:30787800-30789000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:30787800-30789000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:30787800-30789000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr16:30787800-30789000	Enhancers	NHLF	lung
18	chr16:30787800-30789200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr16:30787800-30789400	Enhancers	Liver	Liver
20	chr16:30787800-30789400	Enhancers	Ovary	ovary
21	chr16:30787800-30789400	Enhancers	Pancreas	Pancrea
22	chr16:30787800-30789600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:30787800-30789800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:30787800-30789800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:30787800-30789800	Enhancers	Psoas Muscle	Psoas
26	chr16:30787800-30790000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr16:30787800-30790400	Weak transcription	Fetal Brain Female	brain
28	chr16:30787800-30790400	Enhancers	Right Ventricle	heart
29	chr16:30787800-30790400	Enhancers	HSMMtube	muscle
30	chr16:30787800-30790600	Enhancers	Adipose Nuclei	Adipose
31	chr16:30787800-30791000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr16:30787800-30791000	Weak transcription	Osteobl	bone
33	chr16:30787800-30791400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:30787800-30792800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr16:30787800-30793000	Weak transcription	Brain Anterior Caudate	brain
36	chr16:30787800-30793000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:30787800-30793000	Weak transcription	Thymus	Thymus
38	chr16:30787800-30793800	Weak transcription	Brain Substantia Nigra	brain
39	chr16:30787800-30794400	Weak transcription	Primary T cells from cord blood	blood
40	chr16:30787800-30797200	Weak transcription	HMEC	breast
41	chr16:30787800-30797200	Weak transcription	HUVEC	blood vessel
42	chr16:30787800-30797400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:30787800-30797400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr16:30788000-30788800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr16:30788000-30788800	Flanking Active TSS	Dnd41	blood
46	chr16:30788000-30788800	Flanking Active TSS	K562	blood
47	chr16:30788000-30789200	Enhancers	Left Ventricle	heart
48	chr16:30788000-30789800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr16:30788000-30790400	Enhancers	Fetal Muscle Trunk	muscle
50	chr16:30788000-30791200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links