Variant report

Variant	rs7954591
Chromosome Location	chr12:58299037-58299038
allele	A/G
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:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58196800..58197842-chr12:58298861..58299712,6	K562	blood:
2	chr12:58298839..58299678-chr5:35963312..35964081,2	MCF-7	breast:
3	chr12:58228517..58230592-chr12:58298078..58299845,2	MCF-7	breast:
4	chr12:58224854..58226524-chr12:58298322..58299858,37	K562	blood:
5	chr12:58131382..58132075-chr12:58298920..58299767,2	MCF-7	breast:
6	chr12:58240255..58240999-chr12:58298870..58299495,2	MCF-7	breast:
7	chr12:58164497..58167475-chr12:58297989..58300788,2	K562	blood:
8	chr12:58215853..58216628-chr12:58298828..58299626,2	MCF-7	breast:
9	chr12:58196855..58197808-chr12:58298546..58299692,9	MCF-7	breast:
10	chr12:58238316..58242683-chr12:58295473..58302602,14	MCF-7	breast:
11	chr12:58225549..58227455-chr12:58294861..58299199,3	MCF-7	breast:
12	chr12:58208021..58208650-chr12:58298908..58299650,2	MCF-7	breast:
13	chr12:58224317..58226991-chr12:58298753..58300053,48	MCF-7	breast:
14	chr12:58175991..58177012-chr12:58298853..58299761,6	MCF-7	breast:
15	chr12:58129311..58130058-chr12:58298904..58299889,3	MCF-7	breast:
16	chr12:58297630..58299144-chr12:58332422..58334699,2	K562	blood:
17	chr12:58209706..58210690-chr12:58298859..58299759,3	K562	blood:
18	chr12:58298965..58299695-chr20:52486173..52486891,2	MCF-7	breast:
19	chr12:58236196..58241196-chr12:58294118..58300852,8	MCF-7	breast:
20	chr12:58230137..58231170-chr12:58298849..58299478,3	K562	blood:
21	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
22	chr12:58298311..58300841-chr12:58328319..58331266,4	MCF-7	breast:
23	chr12:58196809..58197769-chr12:58298831..58299866,14	MCF-7	breast:
24	chr12:58298918..58299799-chr12:58311798..58312758,4	MCF-7	breast:
25	chr12:58208670..58209316-chr12:58298909..58299857,2	MCF-7	breast:
26	chr12:58240067..58240814-chr12:58298844..58299779,2	K562	blood:
27	chr12:58290452..58291289-chr12:58298885..58299685,2	MCF-7	breast:
28	chr12:58150276..58151163-chr12:58298941..58299639,3	K562	blood:
29	chr12:58233992..58236447-chr12:58297834..58300424,2	K562	blood:
30	chr12:58224418..58226286-chr12:58298796..58299791,24	MCF-7	breast:
31	chr12:58176005..58176966-chr12:58298816..58299581,4	MCF-7	breast:

No data

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

Extended variants
information (count: 23 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10877033	0.89[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]
rs11172371	0.82[ASN][1000 genomes]
rs11172372	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172375	0.82[ASN][1000 genomes]
rs11172378	0.83[ASN][1000 genomes]
rs1962047	0.83[ASN][1000 genomes]
rs2002275	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]
rs4237845	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]
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	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7954957	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	0.86[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7954591	RP11-620J15.2	cis	Nerve Tibial	GTEx
rs7954591	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7954591	XRCC6BP1	cis	Whole Blood	GTEx
rs7954591	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs7954591	XRCC6BP1	cis	Thyroid	GTEx
rs7954591	XRCC6BP1	cis	lung	GTEx
rs7954591	XRCC6BP1	cis	Artery Tibial	GTEx
rs7954591	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7954591	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs7954591	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7954591	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs7954591	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7954591	XRCC6BP1	cis	Nerve Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58296800-58299200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:58298000-58299200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:58298200-58299600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:58298200-58300200	Enhancers	Fetal Thymus	thymus
5	chr12:58298800-58299200	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr12:58298800-58299200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:58298800-58299200	Active TSS	Right Atrium	heart
8	chr12:58298800-58299600	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:58298800-58299600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:58298800-58299600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:58298800-58299600	Enhancers	Fetal Muscle Trunk	muscle
12	chr12:58298800-58299600	Enhancers	Placenta	Placenta
13	chr12:58298800-58299600	Enhancers	Dnd41	blood
14	chr12:58298800-58299600	Enhancers	Hela-S3	cervix
15	chr12:58298800-58299800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:58299000-58299200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:58299000-58299200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:58299000-58299200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
19	chr12:58299000-58299200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:58299000-58299200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr12:58299000-58299200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr12:58299000-58299200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:58299000-58299200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:58299000-58299200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr12:58299000-58299200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr12:58299000-58299200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr12:58299000-58299200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:58299000-58299200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:58299000-58299200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:58299000-58299200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:58299000-58299200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr12:58299000-58299200	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr12:58299000-58299200	Enhancers	GM12878-XiMat	blood
34	chr12:58299000-58299200	Flanking Active TSS	HepG2	liver
35	chr12:58299000-58299200	Enhancers	HSMM	muscle
36	chr12:58299000-58299200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr12:58299000-58299200	Enhancers	NHDF-Ad	bronchial
38	chr12:58299000-58299200	Flanking Active TSS	Osteobl	bone
39	chr12:58299000-58299400	Enhancers	Primary B cells from cord blood	blood
40	chr12:58299000-58299400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:58299000-58299400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:58299000-58299400	Enhancers	Brain Anterior Caudate	brain
43	chr12:58299000-58299400	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr12:58299000-58299400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr12:58299000-58299400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:58299000-58299400	Flanking Active TSS	Fetal Kidney	kidney
47	chr12:58299000-58299400	Enhancers	Fetal Muscle Leg	muscle
48	chr12:58299000-58299400	Enhancers	Stomach Mucosa	stomach
49	chr12:58299000-58299400	Enhancers	A549	lung
50	chr12:58299000-58299400	Enhancers	NH-A	brain

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