Variant report

Variant	rs2912016
Chromosome Location	chr8:6479178-6479179
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr8:6478881-6479182	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:6479163-6479213	AG10803	skin:	n/a
2	chr8:6479163-6479213	SK-N-MC	brain:	n/a
3	chr8:6479163-6479213	AG09309	skin:	n/a
4	chr8:6479163-6479213	LNCaP	prostate:	n/a
5	chr8:6479163-6479213	NHDF-neo	bronchial:	n/a
6	chr8:6479163-6479213	Hela-S3	cervix:	n/a
7	chr8:6479163-6479213	PrEC	prostate:	n/a
8	chr8:6479163-6479213	GM12891	blood:	n/a
9	chr8:6479163-6479213	HIPEpiC	eye:	n/a
10	chr8:6479163-6479213	HCF	heart:	n/a
11	chr8:6479163-6479213	BE2_C	brain:	n/a
12	chr8:6479163-6479213	NHBE	bronchial:	n/a
13	chr8:6479163-6479213	HPAEpiC	pulmonary alveolar:	n/a
14	chr8:6479163-6479213	HRCEpiC	kidney:	n/a
15	chr8:6479163-6479213	HUVEC	blood vessel:	n/a
16	chr8:6479163-6479213	U87	brain:	n/a
17	chr8:6479163-6479213	SKMC	muscle:	n/a
18	chr8:6479163-6479213	HNPCEpiC	eye:	n/a
19	chr8:6479163-6479213	AG09319	gingival:	n/a
20	chr8:6479163-6479213	NH-A	brain:	n/a
21	chr8:6479163-6479213	HEEpiC	esophagus:	n/a
22	chr8:6479163-6479213	IMR90	lung:	fetal
23	chr8:6479163-6479213	HCM	heart:	n/a
24	chr8:6479163-6479213	RPTEC	kidney:	n/a
25	chr8:6479163-6479213	MCF10A-Er-Src	breast:	n/a
26	chr8:6479163-6479213	GM12892	blood:	n/a
27	chr8:6479163-6479213	Jurkat	blood:	n/a
28	chr8:6479163-6479213	A549	lung:	n/a
29	chr8:6479163-6479213	HCT-116	colon:	n/a
30	chr8:6479163-6479213	T-47D	breast:	n/a
31	chr8:6479163-6479213	MCF-7	breast:	n/a
32	chr8:6479163-6479213	AG04449	skin:	fetal
33	chr8:6479163-6479213	SAEC	small airway:	n/a
34	chr8:6479163-6479213	HL-60	blood:	n/a
35	chr8:6479163-6479213	ovcar-3	ovarian:	n/a
36	chr8:6479163-6479213	HAEpiC	amniotic membrane:	n/a
37	chr8:6479163-6479213	SK-N-SH	brain:	n/a
38	chr8:6479163-6479213	HCPEpiC	choroid plexus:	n/a
39	chr8:6479163-6479213	AG04450	lung:	fetal
40	chr8:6479163-6479213	BJ	skin:	n/a
41	chr8:6479163-6479213	SK-N-SH_RA	brain:	n/a
42	chr8:6479163-6479213	ProgFib	skin:	n/a
43	chr8:6479163-6479213	AoSMC	blood vessel:	n/a
44	chr8:6479163-6479213	CMK	blood:	n/a
45	chr8:6479163-6479213	NB4	blood:	n/a
46	chr8:6479163-6479213	HRE	kidney:	n/a
47	chr8:6479163-6479213	Caco-2	colon:	n/a
48	chr8:6479163-6479213	ECC-1	luminal epithelium:	n/a
49	chr8:6479163-6479213	Hepatocyte	liver:	n/a
50	chr8:6479163-6479213	NT2-D1	testis:	n/a

No data

Variant related genes	Relation type
ENSG00000271743	TF binding region
ENSG00000271743	CpG island

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1057090	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs11137038	0.82[GIH][hapmap]
rs11137041	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11998083	0.81[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2011423	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912010	0.82[CEU][hapmap]
rs2912064	0.81[CEU][hapmap]
rs2936501	0.81[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2959798	0.81[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2959799	0.81[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs3020259	0.95[CEU][hapmap];0.85[EUR][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	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
12	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2912016	MCPH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6457200-6479200	Weak transcription	Brain Germinal Matrix	brain
2	chr8:6457400-6479200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:6457800-6479200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:6458000-6498400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:6458600-6479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr8:6461400-6479800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:6464800-6481000	Weak transcription	Primary B cells from cord blood	blood
8	chr8:6468600-6479200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr8:6469000-6479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:6469000-6479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:6469000-6479400	Weak transcription	Aorta	Aorta
12	chr8:6469000-6479400	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:6472400-6486200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:6474000-6481400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:6474200-6479400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:6474200-6479400	Weak transcription	Fetal Brain Female	brain
17	chr8:6474200-6486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:6474200-6505200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr8:6474400-6479200	Weak transcription	Fetal Intestine Large	intestine
20	chr8:6474400-6479200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:6474400-6481400	Weak transcription	Left Ventricle	heart
22	chr8:6474600-6481200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr8:6474600-6483000	Weak transcription	Fetal Lung	lung
24	chr8:6474600-6488800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr8:6474800-6479200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:6474800-6479200	Weak transcription	NHEK	skin
27	chr8:6474800-6481400	Weak transcription	HSMMtube	muscle
28	chr8:6474800-6483600	Weak transcription	Fetal Heart	heart
29	chr8:6474800-6483600	Weak transcription	K562	blood
30	chr8:6474800-6498400	Weak transcription	HSMM	muscle
31	chr8:6475000-6480000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr8:6475200-6479200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:6475200-6481400	Weak transcription	Right Atrium	heart
34	chr8:6475200-6482800	Weak transcription	Hela-S3	cervix
35	chr8:6475400-6479200	Weak transcription	Brain Substantia Nigra	brain
36	chr8:6476200-6484400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:6476400-6499000	Weak transcription	Brain Angular Gyrus	brain
38	chr8:6476400-6502800	Weak transcription	Colonic Mucosa	Colon
39	chr8:6477600-6479600	Weak transcription	HepG2	liver
40	chr8:6477600-6481400	Weak transcription	Ovary	ovary
41	chr8:6477600-6485400	Strong transcription	Dnd41	blood
42	chr8:6477800-6480200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:6477800-6483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:6477800-6483400	Weak transcription	Osteobl	bone
45	chr8:6478000-6479600	Strong transcription	Thymus	Thymus
46	chr8:6478000-6482800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr8:6478000-6487400	Weak transcription	Small Intestine	intestine
48	chr8:6478200-6480200	Strong transcription	Fetal Thymus	thymus
49	chr8:6478200-6480200	Strong transcription	GM12878-XiMat	blood
50	chr8:6478200-6484800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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