Variant report

Variant	rs848616
Chromosome Location	chr2:36811467-36811468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36809435..36813840-chr2:36817141..36820574,5	K562	blood:
2	chr2:36810053..36812056-chr2:36823147..36825466,2	K562	blood:

Variant related genes	Relation type
ENSG00000171055	Chromatin interaction
ENSG00000256845	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10175266	0.82[EUR][1000 genomes]
rs10178965	0.84[EUR][1000 genomes]
rs10180760	0.84[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10189554	0.88[EUR][1000 genomes]
rs10194100	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10197570	0.88[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10469897	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10469898	0.96[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11124519	0.85[EUR][1000 genomes]
rs11686443	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11691600	1.00[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs11691767	0.83[CEU][hapmap]
rs11693359	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12105545	0.96[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs13029475	0.85[EUR][1000 genomes]
rs13385408	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13398345	0.90[EUR][1000 genomes]
rs13406169	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13406184	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13410783	0.84[EUR][1000 genomes]
rs14291	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523786	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1533946	0.88[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1533947	0.80[EUR][1000 genomes]
rs1533948	0.88[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1533949	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17019087	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs17488036	0.84[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2022211	0.88[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2072533	0.91[EUR][1000 genomes]
rs2072534	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2072535	0.96[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2075226	0.96[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2110986	0.91[EUR][1000 genomes]
rs2110987	0.84[EUR][1000 genomes]
rs2160403	0.85[EUR][1000 genomes]
rs2160404	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs34392255	0.93[EUR][1000 genomes]
rs34425257	0.88[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs3770788	0.93[EUR][1000 genomes]
rs3770797	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs3770799	0.83[EUR][1000 genomes]
rs3770809	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs3770811	0.88[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs55700228	0.89[EUR][1000 genomes]
rs57670037	0.83[EUR][1000 genomes]
rs6728602	0.89[EUR][1000 genomes]
rs848610	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs848611	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848612	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs848613	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848614	0.88[EUR][1000 genomes]
rs848619	1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs848624	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs848627	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs848629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs848630	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs848631	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs848635	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs848636	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs848638	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs848639	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs848640	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9917316	0.90[EUR][1000 genomes]
rs9917318	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs848616	FEZ2	cis	parietal	SCAN
rs848616	FEZ2	cis	Cerebellum	GTEx
rs848616	CRIM1	cis	cerebellum	SCAN
rs848616	FEZ2	cis	cerebellum	SCAN
rs848616	SLC8A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
3	chr2:36790800-36812000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:36799200-36812800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:36799400-36812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
22	chr2:36800200-36817600	Strong transcription	Liver	Liver
23	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
24	chr2:36801400-36813200	Strong transcription	Fetal Lung	lung
25	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:36801800-36812200	Strong transcription	Fetal Thymus	thymus
28	chr2:36801800-36813800	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:36801800-36814600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:36802400-36815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:36802800-36812400	Strong transcription	NH-A	brain
37	chr2:36803200-36813400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:36803400-36812000	Strong transcription	HMEC	breast
39	chr2:36803600-36818000	Strong transcription	Dnd41	blood
40	chr2:36803800-36814600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:36804400-36812400	Strong transcription	Adipose Nuclei	Adipose
42	chr2:36804400-36812800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:36804600-36814000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:36804600-36814200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:36804600-36814800	Strong transcription	Primary B cells from cord blood	blood
46	chr2:36805000-36812000	Strong transcription	NHDF-Ad	bronchial
47	chr2:36805400-36812400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:36806000-36812400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:36806200-36812600	Strong transcription	Primary T cells from cord blood	blood
50	chr2:36806200-36814000	Weak transcription	Placenta Amnion	Placenta Amnion

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