Variant report

Variant	rs12566948
Chromosome Location	chr1:227974279-227974280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227966135..227968360-chr1:227973552..227975937,2	MCF-7	breast:
2	chr1:227973990..227976500-chr1:228134426..228136462,3	MCF-7	breast:
3	chr1:227973508..227976414-chr1:228271906..228274660,2	K562	blood:
4	chr1:227945394..227947244-chr1:227973849..227976801,2	MCF-7	breast:
5	chr1:227962656..227964965-chr1:227972636..227975785,3	MCF-7	breast:
6	chr1:227960240..227967392-chr1:227972741..227977657,8	K562	blood:
7	chr1:227973847..227976813-chr1:228134403..228136465,4	MCF-7	breast:
8	chr1:227970651..227973164-chr1:227973342..227975838,2	K562	blood:
9	chr1:227968386..227970140-chr1:227972618..227974826,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12563117	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12564736	1.00[ASN][1000 genomes]
rs12564929	1.00[ASN][1000 genomes]
rs12565099	1.00[CHB][hapmap]
rs12565109	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12566716	1.00[ASN][1000 genomes]
rs1323021	1.00[CHB][hapmap]
rs13373816	1.00[ASN][1000 genomes]
rs1570429	0.89[CEU][hapmap]
rs16841323	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16847987	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16848110	0.89[CEU][hapmap]
rs2273936	0.89[CEU][hapmap]
rs3806264	0.89[CEU][hapmap]
rs41305134	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60156730	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60255904	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6684706	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748405	0.89[CEU][hapmap]
rs996226	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers 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	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12566948	C1orf35	cis	parietal	SCAN
rs12566948	HIST3H2A	cis	parietal	SCAN
rs12566948	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs12566948	HIST3H2A	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
2	chr1:227954400-227974600	Weak transcription	HMEC	breast
3	chr1:227955800-227974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:227955800-227975200	Weak transcription	Hela-S3	cervix
5	chr1:227956000-227974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:227957800-227974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227958000-227975200	Weak transcription	A549	lung
8	chr1:227964400-227975000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:227967800-227974800	Weak transcription	NH-A	brain
10	chr1:227969200-227974800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:227969400-227974800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:227970400-227974400	Weak transcription	Liver	Liver
13	chr1:227970400-227974400	Weak transcription	HSMMtube	muscle
14	chr1:227970400-227974600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227970400-227974600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:227970400-227974600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:227970400-227974800	Weak transcription	Dnd41	blood
18	chr1:227970400-227975000	Weak transcription	Aorta	Aorta
19	chr1:227970600-227975400	Weak transcription	K562	blood
20	chr1:227973200-227975000	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:227973400-227974400	Enhancers	Pancreas	Pancrea
22	chr1:227973400-227974600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:227973400-227974800	Enhancers	Primary B cells from cord blood	blood
24	chr1:227973400-227974800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:227973400-227974800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:227973400-227974800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:227973400-227974800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:227973400-227974800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:227973400-227974800	Enhancers	GM12878-XiMat	blood
30	chr1:227973400-227975000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:227973400-227975000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:227973400-227975000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:227973400-227975200	Bivalent Enhancer	Fetal Thymus	thymus
34	chr1:227973600-227974400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:227973600-227974400	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr1:227973600-227974400	Enhancers	Colonic Mucosa	Colon
37	chr1:227973600-227974600	Enhancers	Gastric	stomach
38	chr1:227973600-227974600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
39	chr1:227973600-227974800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr1:227973600-227974800	Enhancers	Left Ventricle	heart
41	chr1:227973600-227974800	Enhancers	Right Ventricle	heart
42	chr1:227973600-227975000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr1:227973600-227975000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr1:227973600-227975800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr1:227973600-227975800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr1:227973800-227974400	Enhancers	Brain Anterior Caudate	brain
47	chr1:227973800-227974400	Bivalent Enhancer	Fetal Stomach	stomach
48	chr1:227973800-227974600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:227973800-227974600	Bivalent Enhancer	Fetal Intestine Small	intestine
50	chr1:227973800-227974600	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links