Variant report

Variant	rs28634361
Chromosome Location	chr2:134326963-134326964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:134326913-134326963	BJ	skin:	n/a
2	chr2:134326913-134326963	CMK	blood:	n/a
3	chr2:134326913-134326963	SK-N-SH	brain:	n/a
4	chr2:134326913-134326963	NB4	blood:	n/a
5	chr2:134326913-134326963	HCM	heart:	n/a
6	chr2:134326913-134326963	HMEC	breast:	n/a
7	chr2:134326913-134326963	SK-N-SH_RA	brain:	n/a
8	chr2:134326913-134326963	GM12878	blood:	n/a
9	chr2:134326913-134326963	AG09309	skin:	n/a
10	chr2:134326913-134326963	K562	blood:	n/a
11	chr2:134326913-134326963	NT2-D1	testis:	n/a
12	chr2:134326913-134326963	PrEC	prostate:	n/a
13	chr2:134326913-134326963	Hepatocyte	liver:	n/a
14	chr2:134326913-134326963	HCT-116	colon:	n/a
15	chr2:134326913-134326963	HIPEpiC	eye:	n/a
16	chr2:134326913-134326963	PANC-1	pancreas:	n/a
17	chr2:134326913-134326963	T-47D	breast:	n/a
18	chr2:134326913-134326963	NH-A	brain:	n/a
19	chr2:134326913-134326963	HRPEpiC	eye:	n/a
20	chr2:134326913-134326963	HEK293	kidney:	embryo
21	chr2:134326913-134326963	HUVEC	blood vessel:	n/a
22	chr2:134326913-134326963	HEEpiC	esophagus:	n/a
23	chr2:134326913-134326963	H1-hESC	embryonic stem cell:	embryo
24	chr2:134326913-134326963	HL-60	blood:	n/a
25	chr2:134326913-134326963	AG09319	gingival:	n/a
26	chr2:134326913-134326963	BE2_C	brain:	n/a
27	chr2:134326913-134326963	NHBE	bronchial:	n/a
28	chr2:134326913-134326963	LNCaP	prostate:	n/a
29	chr2:134326913-134326963	NHDF-neo	bronchial:	n/a
30	chr2:134326913-134326963	SKMC	muscle:	n/a
31	chr2:134326913-134326963	HRE	kidney:	n/a
32	chr2:134326913-134326963	AG04449	skin:	fetal
33	chr2:134326913-134326963	GM12892	blood:	n/a
34	chr2:134326913-134326963	Jurkat	blood:	n/a
35	chr2:134326913-134326963	A549	lung:	n/a
36	chr2:134326913-134326963	ProgFib	skin:	n/a
37	chr2:134326913-134326963	HCF	heart:	n/a
38	chr2:134326913-134326963	AG04450	lung:	fetal
39	chr2:134326913-134326963	SAEC	small airway:	n/a
40	chr2:134326913-134326963	MCF10A-Er-Src	breast:	n/a
41	chr2:134326913-134326963	HRCEpiC	kidney:	n/a
42	chr2:134326913-134326963	SK-N-MC	brain:	n/a
43	chr2:134326913-134326963	HPAEpiC	pulmonary alveolar:	n/a
44	chr2:134326913-134326963	AG10803	skin:	n/a
45	chr2:134326913-134326963	GM12891	blood:	n/a
46	chr2:134326913-134326963	GM19239	blood:	n/a
47	chr2:134326913-134326963	HCPEpiC	choroid plexus:	n/a
48	chr2:134326913-134326963	PFSK-1	brain:	n/a
49	chr2:134326913-134326963	Caco-2	colon:	n/a
50	chr2:134326913-134326963	HAEpiC	amniotic membrane:	n/a

No data

Variant related genes	Relation type
NCKAP5	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10172908	1.00[EUR][1000 genomes]
rs10176630	1.00[EUR][1000 genomes]
rs10179509	1.00[EUR][1000 genomes]
rs10180776	1.00[EUR][1000 genomes]
rs10182352	1.00[EUR][1000 genomes]
rs10204302	1.00[EUR][1000 genomes]
rs11904353	1.00[EUR][1000 genomes]
rs13383175	1.00[EUR][1000 genomes]
rs13383603	1.00[EUR][1000 genomes]
rs13396221	1.00[EUR][1000 genomes]
rs13402934	1.00[EUR][1000 genomes]
rs13406195	1.00[EUR][1000 genomes]
rs13406470	1.00[EUR][1000 genomes]
rs13410388	1.00[EUR][1000 genomes]
rs13419194	1.00[EUR][1000 genomes]
rs13432659	1.00[EUR][1000 genomes]
rs1897430	1.00[EUR][1000 genomes]
rs1897431	1.00[EUR][1000 genomes]
rs28420171	1.00[EUR][1000 genomes]
rs6718180	1.00[EUR][1000 genomes]
rs6727895	1.00[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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134324400-134327000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:134324400-134327200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:134324400-134329000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:134324600-134328600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:134324600-134329600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr2:134324600-134330400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:134325000-134330000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:134325000-134342400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:134325200-134329000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:134325400-134331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:134325600-134327000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:134326000-134327200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:134326000-134327600	Enhancers	Fetal Heart	heart
14	chr2:134326000-134328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:134326200-134327000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:134326200-134327000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:134326200-134327000	Enhancers	Stomach Mucosa	stomach
18	chr2:134326200-134327200	Enhancers	Fetal Intestine Small	intestine
19	chr2:134326200-134329600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:134326200-134329800	Weak transcription	Esophagus	oesophagus
21	chr2:134326200-134337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:134326400-134327000	Enhancers	Brain Angular Gyrus	brain
23	chr2:134326400-134327200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:134326400-134327200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:134326400-134327200	Enhancers	Fetal Stomach	stomach
26	chr2:134326400-134327200	Enhancers	NHDF-Ad	bronchial
27	chr2:134326400-134327200	Enhancers	NHLF	lung
28	chr2:134326400-134327400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:134326400-134327400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:134326400-134327400	Enhancers	Fetal Lung	lung
31	chr2:134326400-134327400	Enhancers	NH-A	brain
32	chr2:134326400-134328200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:134326400-134328200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:134326400-134328800	Enhancers	Fetal Kidney	kidney
35	chr2:134326400-134329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:134326400-134330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:134326400-134331800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:134326400-134331800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:134326400-134332400	Weak transcription	Right Atrium	heart
40	chr2:134326400-134334200	Weak transcription	Liver	Liver
41	chr2:134326400-134336200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:134326400-134337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:134326600-134327000	Enhancers	Fetal Brain Female	brain
44	chr2:134326600-134327200	Enhancers	Brain Substantia Nigra	brain
45	chr2:134326600-134327200	Enhancers	Fetal Brain Male	brain
46	chr2:134326600-134328200	Weak transcription	Fetal Intestine Large	intestine
47	chr2:134326600-134328400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:134326600-134331000	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:134326600-134331800	Weak transcription	HUVEC	blood vessel
50	chr2:134326600-134334000	Weak transcription	NHEK	skin

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