Variant report

Variant	rs7954957
Chromosome Location	chr12:58299250-58299251
allele	C/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:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58209675..58210419-chr12:58299140..58299744,2	MCF-7	breast:
2	chr12:58174946..58176646-chr12:58299150..58302148,2	K562	blood:
3	chr12:58196800..58197842-chr12:58298861..58299712,6	K562	blood:
4	chr12:58298839..58299678-chr5:35963312..35964081,2	MCF-7	breast:
5	chr12:58228517..58230592-chr12:58298078..58299845,2	MCF-7	breast:
6	chr12:58152878..58153571-chr12:58299170..58299699,2	MCF-7	breast:
7	chr12:58224854..58226524-chr12:58298322..58299858,37	K562	blood:
8	chr12:58131382..58132075-chr12:58298920..58299767,2	MCF-7	breast:
9	chr12:58240255..58240999-chr12:58298870..58299495,2	MCF-7	breast:
10	chr12:58164497..58167475-chr12:58297989..58300788,2	K562	blood:
11	chr12:58215853..58216628-chr12:58298828..58299626,2	MCF-7	breast:
12	chr12:58196855..58197808-chr12:58298546..58299692,9	MCF-7	breast:
13	chr12:58299223..58301569-chr12:58315233..58317786,2	K562	blood:
14	chr1:145058445..145059351-chr12:58299064..58299785,2	MCF-7	breast:
15	chr12:58238316..58242683-chr12:58295473..58302602,14	MCF-7	breast:
16	chr12:58208021..58208650-chr12:58298908..58299650,2	MCF-7	breast:
17	chr12:58224317..58226991-chr12:58298753..58300053,48	MCF-7	breast:
18	chr12:58175991..58177012-chr12:58298853..58299761,6	MCF-7	breast:
19	chr12:58129311..58130058-chr12:58298904..58299889,3	MCF-7	breast:
20	chr12:58209706..58210690-chr12:58298859..58299759,3	K562	blood:
21	chr12:58298965..58299695-chr20:52486173..52486891,2	MCF-7	breast:
22	chr12:58236196..58241196-chr12:58294118..58300852,8	MCF-7	breast:
23	chr12:58236689..58239049-chr12:58299056..58300765,2	K562	blood:
24	chr12:58230137..58231170-chr12:58298849..58299478,3	K562	blood:
25	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
26	chr12:58298311..58300841-chr12:58328319..58331266,4	MCF-7	breast:
27	chr12:58196809..58197769-chr12:58298831..58299866,14	MCF-7	breast:
28	chr12:58298918..58299799-chr12:58311798..58312758,4	MCF-7	breast:
29	chr12:58208670..58209316-chr12:58298909..58299857,2	MCF-7	breast:
30	chr12:58240067..58240814-chr12:58298844..58299779,2	K562	blood:
31	chr12:58290452..58291289-chr12:58298885..58299685,2	MCF-7	breast:
32	chr12:58150276..58151163-chr12:58298941..58299639,3	K562	blood:
33	chr12:58233992..58236447-chr12:58297834..58300424,2	K562	blood:
34	chr12:58224418..58226286-chr12:58298796..58299791,24	MCF-7	breast:
35	chr12:58176005..58176966-chr12:58298816..58299581,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135452	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000270039	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000269903	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000123297	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10747786	0.93[CHD][hapmap]
rs10747787	0.93[CHD][hapmap]
rs10783855	0.80[CHD][hapmap]
rs10877028	0.80[CHD][hapmap]
rs10877029	0.93[CHD][hapmap]
rs10877030	0.93[CHD][hapmap]
rs10877033	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877034	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172367	0.90[CHD][hapmap]
rs11172371	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs11172372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172375	0.82[ASN][1000 genomes]
rs11172378	0.88[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs1599750	0.80[CHD][hapmap]
rs1962047	0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.88[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs3751330	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs4128707	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237844	0.90[CHD][hapmap]
rs4237845	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417327	0.94[ASN][1000 genomes]
rs4553410	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630335	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs4760172	0.90[CHD][hapmap]
rs4760340	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap]
rs6581157	0.83[ASN][1000 genomes]
rs6650217	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650218	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650219	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306124	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7312623	0.93[CHD][hapmap]
rs7954591	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963992	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7954957	XRCC6BP1	cis	lung	GTEx
rs7954957	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7954957	NCKAP1L	cis	cerebellum	SCAN
rs7954957	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs7954957	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7954957	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs7954957	XRCC6BP1	cis	Nerve Tibial	GTEx
rs7954957	XRCC6BP1	cis	Thyroid	GTEx
rs7954957	XRCC6BP1	cis	Artery Tibial	GTEx
rs7954957	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7954957	XRCC6BP1	cis	Whole Blood	GTEx
rs7954957	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs7954957	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7954957	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs7954957	RP11-620J15.2	cis	Nerve Tibial	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58298200-58299600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:58298200-58300200	Enhancers	Fetal Thymus	thymus
3	chr12:58298800-58299600	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:58298800-58299600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:58298800-58299600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:58298800-58299600	Enhancers	Fetal Muscle Trunk	muscle
7	chr12:58298800-58299600	Enhancers	Placenta	Placenta
8	chr12:58298800-58299600	Enhancers	Dnd41	blood
9	chr12:58298800-58299600	Enhancers	Hela-S3	cervix
10	chr12:58298800-58299800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:58299000-58299400	Enhancers	Primary B cells from cord blood	blood
12	chr12:58299000-58299400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:58299000-58299400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:58299000-58299400	Enhancers	Brain Anterior Caudate	brain
15	chr12:58299000-58299400	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr12:58299000-58299400	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr12:58299000-58299400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr12:58299000-58299400	Flanking Active TSS	Fetal Kidney	kidney
19	chr12:58299000-58299400	Enhancers	Fetal Muscle Leg	muscle
20	chr12:58299000-58299400	Enhancers	Stomach Mucosa	stomach
21	chr12:58299000-58299400	Enhancers	A549	lung
22	chr12:58299000-58299400	Enhancers	NH-A	brain
23	chr12:58299000-58299400	Enhancers	NHLF	lung
24	chr12:58299000-58299600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:58299000-58299600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:58299000-58299600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:58299000-58299600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:58299000-58299600	Enhancers	Primary T cells from cord blood	blood
29	chr12:58299000-58299600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:58299000-58299600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:58299000-58299600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr12:58299000-58299600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:58299000-58299600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:58299000-58299600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:58299000-58299600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:58299000-58299600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:58299000-58299600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:58299000-58299600	Enhancers	Brain Substantia Nigra	brain
39	chr12:58299000-58299600	Enhancers	Colon Smooth Muscle	Colon
40	chr12:58299000-58299600	Enhancers	Duodenum Mucosa	Duodenum
41	chr12:58299000-58299600	Enhancers	Fetal Intestine Large	intestine
42	chr12:58299000-58299600	Enhancers	Fetal Lung	lung
43	chr12:58299000-58299600	Enhancers	Fetal Stomach	stomach
44	chr12:58299000-58299600	Enhancers	Ovary	ovary
45	chr12:58299000-58299600	Enhancers	Psoas Muscle	Psoas
46	chr12:58299000-58299600	Enhancers	Rectal Smooth Muscle	rectum
47	chr12:58299000-58299600	Enhancers	Right Ventricle	heart
48	chr12:58299000-58299600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:58299000-58299600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr12:58299000-58299600	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links