Variant report

Variant	rs2256367
Chromosome Location	chr8:98930457-98930458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:98929263..98931396-chr8:99057196..99059204,2	MCF-7	breast:
2	chr8:98929668..98932562-chr8:98996810..98999331,2	K562	blood:
3	chr8:98929481..98932017-chr8:98944998..98947169,2	MCF-7	breast:
4	chr8:98930453..98932411-chr8:98936573..98938197,2	MCF-7	breast:
5	chr8:98921821..98924732-chr8:98928990..98931932,2	K562	blood:

Variant related genes	Relation type
ENSG00000156482	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1020654	0.82[CEU][hapmap]
rs1020655	0.81[CEU][hapmap]
rs11779647	0.81[MEX][hapmap]
rs12548243	0.88[CEU][hapmap]
rs1378124	0.83[MEX][hapmap]
rs1378125	0.82[CEU][hapmap]
rs1454714	0.83[MEX][hapmap]
rs2444900	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2444903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444904	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2444906	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512068	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2512072	0.82[CEU][hapmap]
rs2513835	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2513837	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2513838	0.82[CEU][hapmap];0.88[MEX][hapmap]
rs2959646	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs6468603	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9693435	0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2256367	NCALD	cis	parietal	SCAN
rs2256367	GAP43	trans	parietal	SCAN
rs2256367	PGCP	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98922000-98930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr8:98923200-98930800	Enhancers	Fetal Muscle Leg	muscle
3	chr8:98925400-98930600	Weak transcription	Placenta	Placenta
4	chr8:98925400-98933200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:98925400-98933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:98926200-98932400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr8:98927200-98931200	Enhancers	Fetal Heart	heart
8	chr8:98928000-98930600	Weak transcription	Esophagus	oesophagus
9	chr8:98928200-98930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr8:98928200-98933200	Weak transcription	Brain Substantia Nigra	brain
11	chr8:98928600-98931400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr8:98928800-98931000	Enhancers	HSMM	muscle
13	chr8:98928800-98931200	Enhancers	NHDF-Ad	bronchial
14	chr8:98928800-98931800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:98929000-98931200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:98929000-98931400	Enhancers	NHLF	lung
17	chr8:98929200-98930800	Weak transcription	Pancreas	Pancrea
18	chr8:98929200-98931000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:98929200-98931400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:98929200-98944800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:98929400-98931000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:98929400-98931000	Enhancers	Right Atrium	heart
23	chr8:98929400-98931200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:98929400-98931200	Enhancers	NH-A	brain
25	chr8:98929400-98931200	Enhancers	Osteobl	bone
26	chr8:98929400-98934800	Weak transcription	Adipose Nuclei	Adipose
27	chr8:98929600-98930600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr8:98929600-98931000	Enhancers	Fetal Muscle Trunk	muscle
29	chr8:98929600-98932800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr8:98929600-98935000	Weak transcription	Fetal Kidney	kidney
31	chr8:98929600-98938000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:98929800-98930800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:98929800-98930800	Weak transcription	Ovary	ovary
34	chr8:98929800-98931600	Enhancers	Fetal Intestine Large	intestine
35	chr8:98929800-98933000	Weak transcription	Brain Anterior Caudate	brain
36	chr8:98929800-98933000	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:98929800-98933200	Weak transcription	Fetal Stomach	stomach
38	chr8:98929800-98936600	Weak transcription	Fetal Lung	lung
39	chr8:98929800-98937800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr8:98930000-98930600	Weak transcription	Lung	lung
41	chr8:98930000-98933200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:98930200-98930600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:98930200-98931200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr8:98930200-98931200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr8:98930200-98931200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:98930200-98931200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr8:98930200-98931600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:98930200-98932000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr8:98930400-98930600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr8:98930400-98930600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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