Variant report

Variant	rs774899
Chromosome Location	chr12:58027081-58027082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:339)
CpG islands
(count:122)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:339 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr12:58026537-58027172	Hela-S3	cervix:	n/a	chr12:58026801-58026811
2	EP300	chr12:58027039-58027282	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:58025843-58027192	K562	blood:	n/a	n/a
4	CTCF	chr12:58026856-58027178	NHEK	skin:	n/a	n/a
5	CTCF	chr12:58026940-58027090	GM12878	blood:	n/a	n/a
6	CTCF	chr12:58026769-58027424	GM12878	blood:	n/a	n/a
7	CHD1	chr12:58026770-58027192	IMR90	lung:	n/a	chr12:58026801-58026811
8	RAD21	chr12:58026644-58027323	SK-N-SH	brain:	n/a	n/a
9	UBTF	chr12:58025989-58027212	K562	blood:	n/a	n/a
10	MYC	chr12:58026810-58027169	NB4	blood:	n/a	n/a
11	HA-E2F1	chr12:58026291-58027200	Hela-S3	cervix:	n/a	n/a
12	ZBTB7A	chr12:58026116-58027326	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr12:58026771-58027235	MCF-7	breast:	n/a	n/a
14	E2F6	chr12:58026755-58027313	A549	lung:	n/a	chr12:58027192-58027201
15	TAF1	chr12:58025793-58027359	H1-neurons	neurons:	n/a	n/a
16	SIN3AK20	chr12:58026588-58027223	PANC-1	pancreas:	n/a	n/a
17	NR2F2	chr12:58026848-58027172	K562	blood:	n/a	n/a
18	MAX	chr12:58026529-58027356	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr12:58026980-58027130	HMF	breast:	n/a	n/a
20	TEAD4	chr12:58026469-58027223	SK-N-SH	brain:	n/a	n/a
21	MAX	chr12:58026674-58027303	SK-N-SH	brain:	n/a	n/a
22	ELK1	chr12:58027043-58027106	K562	blood:	n/a	n/a
23	ZNF143	chr12:58026852-58027170	Hela-S3	cervix:	n/a	chr12:58026901-58026911
24	NR2F2	chr12:58026763-58027386	K562	blood:	n/a	n/a
25	E2F6	chr12:58025823-58027509	A549	lung:	n/a	chr12:58027192-58027201
26	MYC	chr12:58026954-58027087	MCF-7	breast:	n/a	n/a
27	CTCF	chr12:58026859-58027203	GM10248	blood:	n/a	n/a
28	CTCF	chr12:58026665-58027390	MCF-7	breast:	n/a	chr12:58026689-58026702
29	FOXA2	chr12:58026774-58027266	A549	lung:	n/a	n/a
30	CTCF	chr12:58026960-58027110	NHDF-neo	bronchial:	n/a	n/a
31	RAD21	chr12:58026727-58027287	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr12:58026821-58027106	K562	blood:	n/a	chr12:58026899-58026908 chr12:58026830-58026841
33	CTCF	chr12:58026798-58027589	K562	blood:	n/a	n/a
34	CTCF	chr12:58026960-58027110	GM12865	blood:	n/a	n/a
35	EGR1	chr12:58026747-58027280	MCF-7	breast:	n/a	chr12:58027187-58027200
36	CTCF	chr12:58027000-58027150	GM12872	blood:	n/a	n/a
37	REST	chr12:58025251-58027842	H1-neurons	neurons:	n/a	chr12:58026939-58026949 chr12:58025258-58025267 chr12:58026880-58026893
38	SMC3	chr12:58026802-58027202	K562	blood:	n/a	n/a
39	CTCF	chr12:58026840-58027164	K562	blood:	n/a	n/a
40	CREB1	chr12:58026691-58027174	A549	lung:	n/a	n/a
41	CTCF	chr12:58026845-58027160	LNCaP	prostate:	n/a	n/a
42	RUNX3	chr12:58026740-58027185	GM12878	blood:	n/a	n/a
43	TEAD4	chr12:58026711-58027492	K562	blood:	n/a	n/a
44	POLR2A	chr12:58026790-58027140	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:58026960-58027110	GM12866	blood:	n/a	n/a
46	JUND	chr12:58026757-58027226	A549	lung:	n/a	n/a
47	TCF7L2	chr12:58026878-58027191	PANC-1	pancreas:	n/a	n/a
48	RUNX3	chr12:58026761-58027175	GM12878	blood:	n/a	n/a
49	CTCF	chr12:58026845-58027159	Lung_OC	lung:	n/a	n/a
50	CTCF	chr12:58026940-58027090	HBMEC	blood vessel:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58027055-58027105	AG09319	gingival:	n/a
2	chr12:58027032-58027082	SK-N-SH_RA	brain:	n/a
3	chr12:58027055-58027105	SK-N-SH	brain:	n/a
4	chr12:58027055-58027105	SKMC	muscle:	n/a
5	chr12:58027032-58027082	CMK	blood:	n/a
6	chr12:58027055-58027105	HUVEC	blood vessel:	n/a
7	chr12:58027055-58027105	HL-60	blood:	n/a
8	chr12:58027032-58027082	GM19239	blood:	n/a
9	chr12:58027055-58027105	BE2_C	brain:	n/a
10	chr12:58027055-58027105	MCF-7	breast:	n/a
11	chr12:58027032-58027082	HPAEpiC	pulmonary alveolar:	n/a
12	chr12:58027055-58027105	HPAEpiC	pulmonary alveolar:	n/a
13	chr12:58027055-58027105	SK-N-MC	brain:	n/a
14	chr12:58027055-58027105	A549	lung:	n/a
15	chr12:58027032-58027082	HAEpiC	amniotic membrane:	n/a
16	chr12:58027055-58027105	U87	brain:	n/a
17	chr12:58027055-58027105	Hepatocyte	liver:	n/a
18	chr12:58027055-58027105	GM19239	blood:	n/a
19	chr12:58027032-58027082	Hepatocyte	liver:	n/a
20	chr12:58027055-58027105	AG04450	lung:	fetal
21	chr12:58027055-58027105	GM12892	blood:	n/a
22	chr12:58027032-58027082	HMEC	breast:	n/a
23	chr12:58027055-58027105	SAEC	small airway:	n/a
24	chr12:58027032-58027082	AoSMC	blood vessel:	n/a
25	chr12:58027032-58027082	MCF-7	breast:	n/a
26	chr12:58027055-58027105	GM06990	blood:	n/a
27	chr12:58027032-58027082	ovcar-3	ovarian:	n/a
28	chr12:58027032-58027082	HUVEC	blood vessel:	n/a
29	chr12:58027032-58027082	ProgFib	skin:	n/a
30	chr12:58027032-58027082	RPTEC	kidney:	n/a
31	chr12:58027032-58027082	HRPEpiC	eye:	n/a
32	chr12:58027055-58027105	H1-hESC	embryonic stem cell:	embryo
33	chr12:58027055-58027105	Hela-S3	cervix:	n/a
34	chr12:58027055-58027105	CMK	blood:	n/a
35	chr12:58027032-58027082	Hela-S3	cervix:	n/a
36	chr12:58027032-58027082	HNPCEpiC	eye:	n/a
37	chr12:58027055-58027105	IMR90	lung:	fetal
38	chr12:58027032-58027082	H1-hESC	embryonic stem cell:	embryo
39	chr12:58027055-58027105	HCM	heart:	n/a
40	chr12:58027032-58027082	HCM	heart:	n/a
41	chr12:58027055-58027105	RPTEC	kidney:	n/a
42	chr12:58027055-58027105	AG04449	skin:	fetal
43	chr12:58027032-58027082	Caco-2	colon:	n/a
44	chr12:58027055-58027105	NB4	blood:	n/a
45	chr12:58027055-58027105	ECC-1	luminal epithelium:	n/a
46	chr12:58027055-58027105	PANC-1	pancreas:	n/a
47	chr12:58027032-58027082	GM12878	blood:	n/a
48	chr12:58027055-58027105	HCF	heart:	n/a
49	chr12:58027032-58027082	HEEpiC	esophagus:	n/a
50	chr12:58027032-58027082	GM12891	blood:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57940164..57942070-chr12:58025601..58028102,2	MCF-7	breast:
2	chr12:58026893..58027508-chr12:58087361..58087934,2	K562	blood:
3	chr12:58026571..58028240-chr12:58118727..58121626,2	MCF-7	breast:
4	chr12:58017301..58018862-chr12:58026279..58027788,2	MCF-7	breast:
5	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
6	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:
7	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:
8	chr12:58026407..58027580-chr12:58087150..58087941,5	MCF-7	breast:
9	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
10	chr12:57939451..57941325-chr12:58024374..58027583,3	K562	blood:
11	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:
12	chr12:57915782..57916713-chr12:58026905..58027434,2	MCF-7	breast:
13	chr12:57983391..57985108-chr12:58026747..58028430,2	MCF-7	breast:
14	chr12:58026019..58028946-chr12:58148453..58151531,3	K562	blood:
15	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:

No data

Variant related genes	Relation type
B4GALNT1	TF binding region
B4GALNT1	CpG island
ENSG00000240771	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000135506	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11172290	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs12296706	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12304013	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12318458	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12320537	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12322482	0.85[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2258877	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277323	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs2619468	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619469	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619470	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640607	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34919374	0.83[ASN][1000 genomes]
rs35831868	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3899676	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71432310	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715930	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774896	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774897	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3404611	chr12:58026085-58030983	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
5	esv1797714	chr12:58026786-58028934	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
6	nsv511490	chr12:58026786-58035706	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
7	esv3493503	chr12:58026835-58030383	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs774899	NCKAP1L	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58025000-58027600	Active TSS	Brain Angular Gyrus	brain
2	chr12:58025400-58027400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:58025400-58027400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:58025400-58027600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:58025400-58027600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:58025600-58027200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:58025600-58027200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:58025600-58027200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:58025600-58027200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:58025600-58027200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
11	chr12:58025600-58027400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr12:58025600-58027400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:58025600-58027400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:58025600-58027400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:58025600-58027600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:58025600-58027600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:58025600-58027600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:58025600-58027600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:58025800-58027200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr12:58025800-58027200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:58025800-58027200	Bivalent Enhancer	Spleen	Spleen
22	chr12:58025800-58027200	Active TSS	A549	lung
23	chr12:58025800-58027400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:58025800-58027400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:58025800-58027400	Active TSS	Psoas Muscle	Psoas
26	chr12:58025800-58027600	Bivalent Enhancer	Liver	Liver
27	chr12:58026000-58027200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:58026000-58027400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:58026000-58027400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:58026000-58027400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:58026000-58027400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
32	chr12:58026000-58027400	Bivalent Enhancer	Stomach Mucosa	stomach
33	chr12:58026200-58027200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:58026200-58027200	Active TSS	HepG2	liver
35	chr12:58026200-58027200	Bivalent/Poised TSS	Osteobl	bone
36	chr12:58026200-58027400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:58026200-58027400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:58026200-58027400	Active TSS	NHLF	lung
39	chr12:58026200-58027600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
40	chr12:58026400-58027200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:58026400-58027200	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
42	chr12:58026400-58027200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
43	chr12:58026400-58027200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr12:58026600-58027200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
45	chr12:58026600-58027200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
46	chr12:58026600-58027200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr12:58026600-58027200	Flanking Active TSS	Pancreas	Pancrea
48	chr12:58026600-58027200	Flanking Active TSS	Right Ventricle	heart
49	chr12:58026600-58027200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr12:58026600-58027200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links