Variant report

Variant	rs4906363
Chromosome Location	chr14:104210239-104210240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104208629..104211518-chr14:104213200..104216195,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088808	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1187417	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12588797	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12879529	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12879612	0.81[ASN][1000 genomes]
rs12883337	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12885509	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12886637	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888002	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890354	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890430	0.82[EUR][1000 genomes]
rs12890822	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12890837	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12893623	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12894657	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17791722	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34596177	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35085624	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35740217	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3742366	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3861678	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4900597	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4906364	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4906365	0.80[ASN][1000 genomes]
rs4906376	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4906377	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4906378	0.82[EUR][1000 genomes]
rs4906379	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56168984	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6576006	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6576007	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66676135	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66953418	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7142769	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7143885	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7149024	0.81[ASN][1000 genomes]
rs7156697	0.81[ASN][1000 genomes]
rs7156834	0.81[ASN][1000 genomes]
rs722637	0.90[EUR][1000 genomes]
rs8548	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9888591	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv902312	chr14:104155317-104211180	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv470673	chr14:104162263-104219949	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4906363	XRCC3	cis	Whole Blood	GTEx
rs4906363	RP11-73M18.8	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104184200-104214400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:104184400-104211000	Weak transcription	Hela-S3	cervix
3	chr14:104191600-104223800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:104192200-104216600	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:104194200-104211400	Strong transcription	Colonic Mucosa	Colon
6	chr14:104194200-104220400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr14:104194800-104212000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr14:104195800-104215200	Weak transcription	HSMM	muscle
9	chr14:104196000-104214200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr14:104196000-104268000	Weak transcription	Small Intestine	intestine
11	chr14:104198000-104218800	Strong transcription	Gastric	stomach
12	chr14:104198200-104224800	Strong transcription	Left Ventricle	heart
13	chr14:104199400-104211800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr14:104200000-104220200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr14:104200200-104214400	Weak transcription	Aorta	Aorta
16	chr14:104200200-104219600	Weak transcription	A549	lung
17	chr14:104200400-104210400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr14:104200400-104212800	Weak transcription	Osteobl	bone
19	chr14:104200400-104231800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:104200600-104216800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:104201000-104215800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:104201000-104267600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:104201400-104214800	Weak transcription	GM12878-XiMat	blood
24	chr14:104202400-104216200	Weak transcription	Fetal Heart	heart
25	chr14:104203000-104220200	Weak transcription	NHLF	lung
26	chr14:104203200-104216800	Strong transcription	Pancreas	Pancrea
27	chr14:104203200-104220200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:104203200-104224600	Weak transcription	Fetal Brain Male	brain
29	chr14:104203200-104267800	Weak transcription	Psoas Muscle	Psoas
30	chr14:104203400-104213400	Strong transcription	Rectal Smooth Muscle	rectum
31	chr14:104203600-104220600	Strong transcription	Fetal Stomach	stomach
32	chr14:104203800-104212200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr14:104204000-104216200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr14:104204200-104220600	Weak transcription	Colon Smooth Muscle	Colon
35	chr14:104204800-104216400	Strong transcription	Placenta	Placenta
36	chr14:104204800-104216800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr14:104206200-104222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:104206400-104214800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr14:104206400-104217600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:104206600-104213200	Weak transcription	Thymus	Thymus
41	chr14:104206600-104219200	Weak transcription	Stomach Mucosa	stomach
42	chr14:104206800-104219800	Weak transcription	Brain Germinal Matrix	brain
43	chr14:104206800-104222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr14:104207200-104214800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:104207400-104219600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr14:104207600-104210400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:104207600-104210800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr14:104207600-104211400	Strong transcription	HepG2	liver
49	chr14:104207800-104214600	Weak transcription	Fetal Muscle Leg	muscle
50	chr14:104207800-104214800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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