Variant report

Variant	rs848643
Chromosome Location	chr2:36782387-36782388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:36779682-36783569	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:36782132-36782947	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:36782381-36782540	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:36778965-36784323	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:36778885-36782748	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:36778021-36782579	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:36778760-36784779	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:36780515-36782650	PANC-1	pancreas:	n/a	n/a
9	BCL3	chr2:36779978-36784433	A549	lung:	n/a	chr2:36780871-36780880 chr2:36782308-36782317
10	POLR2A	chr2:36780183-36787605	A549	lung:	n/a	n/a
11	POLR2A	chr2:36778741-36783444	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:36782295-36782622	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr2:36780142-36782575	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr2:36782363-36782442	ProgFib	skin:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:36782386-36782436	PrEC	prostate:	n/a
2	chr2:36782386-36782436	AG09309	skin:	n/a
3	chr2:36782386-36782436	HCT-116	colon:	n/a
4	chr2:36782386-36782436	NHBE	bronchial:	n/a
5	chr2:36782386-36782436	SKMC	muscle:	n/a
6	chr2:36782386-36782436	HNPCEpiC	eye:	n/a
7	chr2:36782386-36782436	MCF10A-Er-Src	breast:	n/a
8	chr2:36782386-36782436	H1-hESC	embryonic stem cell:	embryo
9	chr2:36782386-36782436	PFSK-1	brain:	n/a
10	chr2:36782386-36782436	ECC-1	luminal epithelium:	n/a
11	chr2:36782386-36782436	SAEC	small airway:	n/a
12	chr2:36782386-36782436	MCF-7	breast:	n/a
13	chr2:36782386-36782436	NT2-D1	testis:	n/a
14	chr2:36782386-36782436	Hela-S3	cervix:	n/a
15	chr2:36782386-36782436	HIPEpiC	eye:	n/a
16	chr2:36782386-36782436	IMR90	lung:	fetal
17	chr2:36782386-36782436	AG04449	skin:	fetal
18	chr2:36782386-36782436	SK-N-SH_RA	brain:	n/a
19	chr2:36782386-36782436	BJ	skin:	n/a
20	chr2:36782386-36782436	Hepatocyte	liver:	n/a
21	chr2:36782386-36782436	GM12891	blood:	n/a
22	chr2:36782386-36782436	RPTEC	kidney:	n/a
23	chr2:36782386-36782436	NH-A	brain:	n/a
24	chr2:36782386-36782436	HEK293	kidney:	embryo
25	chr2:36782386-36782436	HepG2	liver:	n/a
26	chr2:36782386-36782436	NB4	blood:	n/a
27	chr2:36782386-36782436	HL-60	blood:	n/a
28	chr2:36782386-36782436	ovcar-3	ovarian:	n/a
29	chr2:36782386-36782436	Jurkat	blood:	n/a
30	chr2:36782386-36782436	GM12892	blood:	n/a
31	chr2:36782386-36782436	U87	brain:	n/a
32	chr2:36782386-36782436	GM19239	blood:	n/a
33	chr2:36782386-36782436	GM12878	blood:	n/a
34	chr2:36782386-36782436	HCF	heart:	n/a
35	chr2:36782386-36782436	AG09319	gingival:	n/a
36	chr2:36782386-36782436	HEEpiC	esophagus:	n/a
37	chr2:36782386-36782436	T-47D	breast:	n/a
38	chr2:36782386-36782436	HMEC	breast:	n/a
39	chr2:36782386-36782436	AoSMC	blood vessel:	n/a
40	chr2:36782386-36782436	CMK	blood:	n/a
41	chr2:36782386-36782436	K562	blood:	n/a
42	chr2:36782386-36782436	HCM	heart:	n/a
43	chr2:36782386-36782436	HCPEpiC	choroid plexus:	n/a
44	chr2:36782386-36782436	HAEpiC	amniotic membrane:	n/a
45	chr2:36782386-36782436	LNCaP	prostate:	n/a
46	chr2:36782386-36782436	BE2_C	brain:	n/a
47	chr2:36782386-36782436	HPAEpiC	pulmonary alveolar:	n/a
48	chr2:36782386-36782436	NHDF-neo	bronchial:	n/a
49	chr2:36782386-36782436	SK-N-SH	brain:	n/a
50	chr2:36782386-36782436	HUVEC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36773463..36777195-chr2:36780018..36782805,3	K562	blood:
2	chr2:36781920..36784587-chr2:36788838..36790616,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000217075	TF binding region
ENSG00000217075	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10179862	1.00[CHB][hapmap]
rs10180760	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs10197570	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs10210291	1.00[CHB][hapmap]
rs10469897	0.90[CHB][hapmap]
rs10469898	0.91[CHB][hapmap]
rs1179494	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11894187	0.82[EUR][1000 genomes]
rs11899523	0.86[EUR][1000 genomes]
rs12712507	0.86[CHB][hapmap]
rs12712508	1.00[CHB][hapmap]
rs1533946	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs1533947	0.83[ASN][1000 genomes]
rs1533948	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs17019087	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2022211	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs2072534	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs2072535	0.90[CHB][hapmap]
rs2075226	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs2160404	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2276671	0.83[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs34425257	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs3770796	0.86[EUR][1000 genomes]
rs3770797	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3770809	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs3770811	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs3821150	0.89[EUR][1000 genomes]
rs7570763	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs848603	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848605	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs848606	0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs848607	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs848617	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848642	0.83[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs981355	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs9917316	0.81[ASN][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
rs848643	FEZ2	cis	cerebellum	SCAN
rs848643	FEZ2	cis	multi-tissue	Pritchard
rs848643	FEZ2	cis	lymphoblastoid	seeQTL
rs848643	FEZ2	Cis_1M	lymphoblastoid	RTeQTL
rs848643	CRIM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
3	chr2:36750800-36783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:36753800-36782600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:36762400-36783200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:36762800-36783800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:36763200-36784200	Strong transcription	HepG2	liver
9	chr2:36763200-36785200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr2:36764000-36790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:36764200-36783400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:36764200-36783800	Strong transcription	Fetal Intestine Large	intestine
13	chr2:36764400-36787200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:36764800-36791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:36766000-36791800	Weak transcription	Esophagus	oesophagus
16	chr2:36766400-36788600	Weak transcription	Fetal Brain Male	brain
17	chr2:36766800-36782800	Strong transcription	HMEC	breast
18	chr2:36766800-36783200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:36766800-36783400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:36769200-36782600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:36769800-36790400	Weak transcription	Spleen	Spleen
22	chr2:36771000-36789000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:36771200-36788400	Weak transcription	Stomach Mucosa	stomach
24	chr2:36771400-36802800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:36771800-36782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:36772400-36783800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:36772600-36784200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:36772600-36784400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:36773600-36782800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:36773800-36782800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:36774200-36782800	Strong transcription	Liver	Liver
33	chr2:36774200-36784000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:36774200-36784200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:36774400-36789000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:36774600-36783200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:36776400-36783200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:36776600-36786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:36776600-36792600	Weak transcription	Right Ventricle	heart
40	chr2:36776600-36804800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:36776600-36804800	Weak transcription	Fetal Brain Female	brain
42	chr2:36776800-36782800	Strong transcription	Fetal Stomach	stomach
43	chr2:36777400-36786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:36777400-36786600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:36777400-36790600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:36777400-36795000	Weak transcription	Fetal Heart	heart
47	chr2:36777600-36783800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:36777800-36788000	Weak transcription	Brain Anterior Caudate	brain
49	chr2:36778000-36782600	Strong transcription	NH-A	brain
50	chr2:36778200-36782600	Strong transcription	Brain Cingulate Gyrus	brain

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