Variant report

Variant	rs715930
Chromosome Location	chr12:58023981-58023982
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58023964-58024014	NH-A	brain:	n/a
2	chr12:58023964-58024014	Caco-2	colon:	n/a
3	chr12:58023964-58024014	HUVEC	blood vessel:	n/a
4	chr12:58023964-58024014	Hela-S3	cervix:	n/a
5	chr12:58023964-58024014	U87	brain:	n/a
6	chr12:58023964-58024014	AG09319	gingival:	n/a
7	chr12:58023964-58024014	IMR90	lung:	fetal
8	chr12:58023964-58024014	HRE	kidney:	n/a
9	chr12:58023964-58024014	HCM	heart:	n/a
10	chr12:58023964-58024014	RPTEC	kidney:	n/a
11	chr12:58023964-58024014	GM19239	blood:	n/a
12	chr12:58023964-58024014	NT2-D1	testis:	n/a
13	chr12:58023964-58024014	HCPEpiC	choroid plexus:	n/a
14	chr12:58023964-58024014	ProgFib	skin:	n/a
15	chr12:58023964-58024014	SK-N-SH_RA	brain:	n/a
16	chr12:58023964-58024014	AG04449	skin:	fetal
17	chr12:58023964-58024014	NHDF-neo	bronchial:	n/a
18	chr12:58023964-58024014	BJ	skin:	n/a
19	chr12:58023964-58024014	GM12891	blood:	n/a
20	chr12:58023964-58024014	GM12878	blood:	n/a
21	chr12:58023964-58024014	HRCEpiC	kidney:	n/a
22	chr12:58023964-58024014	Jurkat	blood:	n/a
23	chr12:58023964-58024014	H1-hESC	embryonic stem cell:	embryo
24	chr12:58023964-58024014	NB4	blood:	n/a
25	chr12:58023964-58024014	HNPCEpiC	eye:	n/a
26	chr12:58023964-58024014	HMEC	breast:	n/a
27	chr12:58023964-58024014	CMK	blood:	n/a
28	chr12:58023964-58024014	PrEC	prostate:	n/a
29	chr12:58023964-58024014	MCF-7	breast:	n/a
30	chr12:58023964-58024014	SK-N-MC	brain:	n/a
31	chr12:58023964-58024014	HCF	heart:	n/a
32	chr12:58023964-58024014	AG04450	lung:	fetal
33	chr12:58023964-58024014	HEEpiC	esophagus:	n/a
34	chr12:58023964-58024014	BE2_C	brain:	n/a
35	chr12:58023964-58024014	HEK293	kidney:	embryo
36	chr12:58023964-58024014	HL-60	blood:	n/a
37	chr12:58023964-58024014	HPAEpiC	pulmonary alveolar:	n/a
38	chr12:58023964-58024014	SAEC	small airway:	n/a
39	chr12:58023964-58024014	HIPEpiC	eye:	n/a
40	chr12:58023964-58024014	LNCaP	prostate:	n/a
41	chr12:58023964-58024014	ECC-1	luminal epithelium:	n/a
42	chr12:58023964-58024014	T-47D	breast:	n/a
43	chr12:58023964-58024014	ovcar-3	ovarian:	n/a
44	chr12:58023964-58024014	AG09309	skin:	n/a
45	chr12:58023964-58024014	HAEpiC	amniotic membrane:	n/a
46	chr12:58023964-58024014	A549	lung:	n/a
47	chr12:58023964-58024014	AoSMC	blood vessel:	n/a
48	chr12:58023964-58024014	SKMC	muscle:	n/a
49	chr12:58023964-58024014	GM06990	blood:	n/a
50	chr12:58023964-58024014	HRPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:
2	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:

No data

Variant related genes	Relation type
B4GALNT1	CpG island
ENSG00000166986	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11172290	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12304013	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12318458	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320537	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322482	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2258877	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277323	0.90[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619468	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2619469	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2619470	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2640607	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34919374	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35831868	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3899676	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71432310	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774896	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774897	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774898	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774899	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs715930	XRCC6BP1	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58017000-58025000	Weak transcription	K562	blood
2	chr12:58018000-58024600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:58018800-58024000	Strong transcription	Brain Germinal Matrix	brain
4	chr12:58018800-58024200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:58019400-58025200	Weak transcription	Hela-S3	cervix
6	chr12:58020400-58024800	Weak transcription	HepG2	liver
7	chr12:58020600-58024800	Strong transcription	A549	lung
8	chr12:58020600-58026200	Weak transcription	Aorta	Aorta
9	chr12:58020800-58025200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:58021400-58025600	Weak transcription	HMEC	breast
11	chr12:58021600-58024000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:58021600-58024800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:58022000-58025600	Weak transcription	Pancreas	Pancrea
14	chr12:58022200-58024400	ZNF genes & repeats	Fetal Brain Female	brain
15	chr12:58022600-58024200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:58022600-58025600	Weak transcription	Gastric	stomach
17	chr12:58023000-58025600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:58023200-58024000	Enhancers	Brain Hippocampus Middle	brain
19	chr12:58023200-58024800	Enhancers	Brain Anterior Caudate	brain
20	chr12:58023400-58024000	Genic enhancers	Brain Angular Gyrus	brain
21	chr12:58023400-58024200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:58023400-58024200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr12:58023400-58024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:58023400-58025400	Enhancers	Brain Cingulate Gyrus	brain
25	chr12:58023800-58024000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:58023800-58024000	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr12:58023800-58024000	Bivalent Enhancer	Fetal Brain Male	brain
28	chr12:58023800-58024800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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