Variant report

Variant	rs2305022
Chromosome Location	chr8:6272399-6272400
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:6260743..6265726-chr8:6271007..6273930,5	K562	blood:
2	chr8:6266687..6268429-chr8:6271780..6273371,2	K562	blood:

Variant related genes	Relation type
ENSG00000246089	Chromatin interaction
ENSG00000147316	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1054073	0.81[TSI][hapmap]
rs1129703	0.82[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1129706	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11985850	0.92[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs12115169	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12546890	0.85[GIH][hapmap]
rs12674488	0.89[JPT][hapmap]
rs12679619	0.84[JPT][hapmap]
rs13248420	0.84[JPT][hapmap]
rs13281967	0.84[JPT][hapmap]
rs13282022	0.84[JPT][hapmap]
rs13282577	0.84[JPT][hapmap]
rs1373306	0.80[TSI][hapmap]
rs1530408	0.90[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1530409	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs1550690	0.82[JPT][hapmap]
rs1550697	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs1550698	0.94[EUR][1000 genomes]
rs17076812	0.81[CEU][hapmap]
rs17077067	0.84[JPT][hapmap]
rs17077083	0.84[JPT][hapmap]
rs17077094	0.84[JPT][hapmap]
rs17613024	0.84[JPT][hapmap]
rs1867385	0.81[TSI][hapmap]
rs1867386	0.84[TSI][hapmap]
rs1868551	0.82[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1966818	0.90[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1968585	0.83[EUR][1000 genomes]
rs2034143	0.82[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs2053618	0.81[EUR][1000 genomes]
rs2120483	0.94[EUR][1000 genomes]
rs2251956	0.84[JPT][hapmap]
rs2254903	0.84[JPT][hapmap]
rs2277136	0.84[JPT][hapmap]
rs2440406	0.84[JPT][hapmap]
rs2440414	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs2440416	0.84[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2440423	0.84[JPT][hapmap]
rs2440424	0.84[JPT][hapmap]
rs2440427	0.83[JPT][hapmap]
rs2440432	0.84[JPT][hapmap]
rs2440443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440444	0.92[CHB][hapmap];0.90[CHD][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs2440448	0.94[EUR][1000 genomes]
rs2440452	0.82[GIH][hapmap]
rs2442485	0.84[JPT][hapmap]
rs2442502	0.85[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2442510	0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2442511	0.84[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2442512	0.81[EUR][1000 genomes]
rs2442518	0.85[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs2442522	0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2442523	0.83[JPT][hapmap]
rs2442524	0.83[JPT][hapmap];0.80[TSI][hapmap]
rs2442527	0.83[EUR][1000 genomes]
rs2442530	0.82[EUR][1000 genomes]
rs2442533	0.85[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs2442536	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2442546	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2515491	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2515555	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2515564	0.94[JPT][hapmap]
rs2515565	0.94[JPT][hapmap]
rs2515568	0.81[EUR][1000 genomes]
rs2515572	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs2916741	0.91[GIH][hapmap]
rs2916742	0.85[GIH][hapmap]
rs2916743	0.91[GIH][hapmap]
rs2916746	0.91[GIH][hapmap]
rs2916750	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2920660	0.91[GIH][hapmap];0.80[TSI][hapmap]
rs2920674	0.84[JPT][hapmap]
rs2920681	0.84[JPT][hapmap]
rs2922818	0.91[GIH][hapmap]
rs2922820	0.91[GIH][hapmap]
rs60526807	0.94[EUR][1000 genomes]
rs61048567	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6559160	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs6559161	0.89[JPT][hapmap]
rs6559162	1.00[MEX][hapmap];0.80[TSI][hapmap]
rs6559164	0.84[JPT][hapmap]
rs6994734	0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs6995735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7002187	0.84[JPT][hapmap];0.90[MEX][hapmap];0.80[EUR][1000 genomes]
rs7002495	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs7002509	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7008037	0.90[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7008227	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7009134	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73196750	0.81[EUR][1000 genomes]
rs7824209	0.91[GIH][hapmap]
rs894888	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs963754	0.83[JPT][hapmap]
rs9692902	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	nsv1018782	chr8:5984032-6284373	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv949501	chr8:6081704-6303511	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv890041	chr8:6084048-6274963	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv1024103	chr8:6124125-6303511	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1026950	chr8:6127991-6303511	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1025734	chr8:6128828-6303511	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1022940	chr8:6128828-6304814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv527005	chr8:6129051-6287170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1028552	chr8:6129221-6303511	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1021800	chr8:6144798-6286635	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1026004	chr8:6144798-6307692	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv539431	chr8:6144798-6307692	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv933107	chr8:6173244-6312807	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1018882	chr8:6204857-6289937	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv531468	chr8:6248682-6309194	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1033935	chr8:6262180-6275753	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv524404	chr8:6263083-6291485	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv1030323	chr8:6268228-6279511	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2305022	MCPH1	Cis_1M	lymphoblastoid	RTeQTL
rs2305022	MSRA	cis	parietal	SCAN
rs2305022	AGPAT5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6272600	Weak transcription	Esophagus	oesophagus
2	chr8:6265000-6272600	Weak transcription	Gastric	stomach
3	chr8:6265000-6286600	Weak transcription	Small Intestine	intestine
4	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:6265200-6281800	Weak transcription	Right Atrium	heart
6	chr8:6265200-6281800	Weak transcription	Right Ventricle	heart
7	chr8:6265200-6282600	Weak transcription	Colonic Mucosa	Colon
8	chr8:6265200-6302200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr8:6265400-6272600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr8:6265400-6278200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:6265400-6287400	Weak transcription	Psoas Muscle	Psoas
12	chr8:6265400-6303800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:6265600-6276400	Weak transcription	Fetal Brain Male	brain
14	chr8:6265600-6290000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr8:6266000-6275800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:6266000-6275800	Strong transcription	Fetal Muscle Leg	muscle
17	chr8:6266600-6275200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:6266800-6272800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:6266800-6273400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr8:6266800-6274200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr8:6267000-6272800	Strong transcription	Brain Cingulate Gyrus	brain
22	chr8:6267000-6273800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:6267400-6272400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:6267600-6276000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr8:6267600-6291400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr8:6267600-6302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr8:6268200-6282800	Weak transcription	NHLF	lung
28	chr8:6268200-6287400	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:6268400-6272400	Weak transcription	NHEK	skin
30	chr8:6268400-6273800	Weak transcription	Brain Angular Gyrus	brain
31	chr8:6268400-6282800	Weak transcription	Fetal Kidney	kidney
32	chr8:6268600-6273800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr8:6268800-6272400	Weak transcription	Adipose Nuclei	Adipose
34	chr8:6268800-6272400	Weak transcription	Spleen	Spleen
35	chr8:6268800-6272600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr8:6268800-6291600	Weak transcription	HSMMtube	muscle
37	chr8:6269000-6278200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr8:6269200-6272400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:6269200-6273600	Weak transcription	Brain Substantia Nigra	brain
40	chr8:6269200-6275000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:6269400-6272400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr8:6269400-6274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr8:6269400-6281600	Weak transcription	Fetal Heart	heart
44	chr8:6269400-6281800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr8:6269600-6273800	Weak transcription	HMEC	breast
46	chr8:6269600-6278800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr8:6269600-6280200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:6269600-6282800	Weak transcription	HSMM	muscle
49	chr8:6269800-6272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:6269800-6272400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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