Variant report

Variant	rs6509955
Chromosome Location	chr19:56215184-56215185
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	MXI1	chr19:56215146-56215379	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr19:56215180-56215303	SK-N-SH_RA	brain:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
3	MAX	chr19:56214994-56215470	A549	lung:	n/a	n/a
4	CTCF	chr19:56215121-56215386	K562	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
5	EP300	chr19:56215102-56215377	K562	blood:	n/a	n/a
6	CTCF	chr19:56215140-56215290	BJ	skin:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
7	CTCF	chr19:56215141-56215394	GM19238	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
8	CTCF	chr19:56215180-56215330	K562	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
9	MAZ	chr19:56215109-56215429	K562	blood:	n/a	n/a
10	RAD21	chr19:56215138-56215400	K562	blood:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
11	CTCF	chr19:56215146-56215352	LNCaP	prostate:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
12	CTCF	chr19:56215107-56215396	Spleen_OC	spleen:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
13	CTCF	chr19:56215139-56215417	GM12878	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
14	CTCF	chr19:56215160-56215310	HMF	breast:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
15	CTCF	chr19:56215180-56215330	HCPEpiC	choroid plexus:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
16	CTCF	chr19:56215163-56215382	GM19240	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
17	CTCF	chr19:56215160-56215310	HPF	lung:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
18	CTCF	chr19:56215180-56215330	GM12875	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
19	CTCF	chr19:56215160-56215310	HRPEpiC	eye:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
20	CTCF	chr19:56215086-56215437	IMR90	lung:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
21	MAX	chr19:56214933-56215714	H1-hESC	embryonic stem cell:	n/a	chr19:56215523-56215534 chr19:56215523-56215534 chr19:56215526-56215542 chr19:56215524-56215533
22	CTCF	chr19:56215160-56215310	GM12872	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
23	CTCF	chr19:56215180-56215330	HUVEC	blood vessel:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
24	RCOR1	chr19:56215098-56215436	K562	blood:	n/a	n/a
25	CTCF	chr19:56215180-56215330	WERI-Rb-1	eye:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
26	JUND	chr19:56215109-56215410	K562	blood:	n/a	n/a
27	CTCF	chr19:56215072-56215456	K562	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
28	RAD21	chr19:56215129-56215347	K562	blood:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
29	CTCF	chr19:56215180-56215330	AG04449	skin:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
30	CTCF	chr19:56215160-56215310	AG09319	gingival:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
31	SMC3	chr19:56215084-56215408	K562	blood:	n/a	chr19:56215255-56215269
32	CTCF	chr19:56215160-56215310	GM12871	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
33	CTCF	chr19:56215106-56215391	Pancreas_OC	pancreas:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
34	CTCF	chr19:56214975-56215539	HCT-116	colon:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
35	CTCF	chr19:56215153-56215393	MCF-7	breast:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
36	CTCF	chr19:56215180-56215330	HEK293	kidney:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
37	CTCF	chr19:56215160-56215310	GM12865	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
38	MAX	chr19:56215062-56215376	K562	blood:	n/a	n/a
39	POLR2A	chr19:56214997-56220979	K562	blood:	n/a	n/a
40	CTCF	chr19:56215160-56215310	WERI-Rb-1	eye:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
41	CTCF	chr19:56215121-56215381	GM13977	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
42	E2F6	chr19:56214942-56215596	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr19:56215160-56215310	NB4	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
44	CTCF	chr19:56215180-56215330	GM06990	blood:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
45	RAD21	chr19:56215130-56215305	SK-N-SH_RA	brain:	n/a	chr19:56215255-56215269 chr19:56215254-56215273 chr19:56215259-56215271 chr19:56215257-56215270
46	CTCF	chr19:56215180-56215330	HEEpiC	esophagus:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
47	CCNT2	chr19:56215133-56215480	K562	blood:	n/a	n/a
48	HMGN3	chr19:56215121-56215392	K562	blood:	n/a	n/a
49	CTCF	chr19:56215129-56215407	Medullo	brain:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276
50	CTCF	chr19:56215160-56215310	AG04450	lung:	n/a	chr19:56215254-56215270 chr19:56215256-56215269 chr19:56215253-56215271 chr19:56215256-56215269 chr19:56215255-56215276

No.	Distal block	Cell Line	Cell type
1	chr19:56188121..56189803-chr19:56212346..56215225,2	K562	blood:
2	chr19:56185419..56191490-chr19:56212273..56216664,6	K562	blood:
3	chr19:56214734..56218976-chr19:56219559..56224015,5	K562	blood:
4	chr19:56163850..56167887-chr19:56212407..56215372,3	K562	blood:

Variant related genes	Relation type
ENSG00000267865	TF binding region
ENSG00000268593	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000269574	Chromatin interaction
ENSG00000267865	Chromatin interaction
ENSG00000267523	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11673193	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17886456	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4801264	0.82[AMR][1000 genomes]
rs4801265	0.82[CEU][hapmap]
rs504850	0.83[TSI][hapmap]
rs6509952	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8105023	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1057383	chr19:56211031-56456028	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6509955	ZNF256	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
3	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
5	chr19:56200000-56216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:56202600-56217000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:56205800-56215400	Weak transcription	NH-A	brain
8	chr19:56206600-56215400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:56206600-56218600	Weak transcription	HepG2	liver
10	chr19:56207000-56219200	Weak transcription	Psoas Muscle	Psoas
11	chr19:56207400-56215800	Weak transcription	HSMMtube	muscle
12	chr19:56207600-56216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:56207800-56216800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:56208000-56220000	Weak transcription	Fetal Lung	lung
15	chr19:56208200-56215800	Weak transcription	Primary B cells from cord blood	blood
16	chr19:56208400-56215800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:56209000-56217800	Weak transcription	Hela-S3	cervix
18	chr19:56209000-56218000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:56209200-56215400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:56209200-56215800	Weak transcription	Osteobl	bone
21	chr19:56209400-56218200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:56209800-56215400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:56210000-56215200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:56210000-56217800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:56210000-56217800	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:56210000-56218000	Weak transcription	Left Ventricle	heart
27	chr19:56210000-56218400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:56210000-56219600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:56210000-56220000	Weak transcription	Fetal Brain Female	brain
30	chr19:56210200-56216000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:56211200-56215400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:56211200-56218000	Weak transcription	NHEK	skin
33	chr19:56211200-56220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:56212200-56215400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:56212400-56215200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:56212400-56215200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:56212400-56215200	Weak transcription	Spleen	Spleen
38	chr19:56212400-56215400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:56212400-56215600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:56212400-56215800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr19:56212400-56215800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:56212400-56215800	Weak transcription	Colonic Mucosa	Colon
43	chr19:56212400-56215800	Weak transcription	GM12878-XiMat	blood
44	chr19:56212400-56217400	Weak transcription	Thymus	Thymus
45	chr19:56212400-56217600	Weak transcription	Aorta	Aorta
46	chr19:56212400-56217600	Weak transcription	Fetal Muscle Leg	muscle
47	chr19:56212400-56217800	Weak transcription	Brain Germinal Matrix	brain
48	chr19:56212400-56218000	Weak transcription	Brain Anterior Caudate	brain
49	chr19:56212400-56218200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:56212400-56218200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links