Variant report

Variant	rs7154572
Chromosome Location	chr14:104105414-104105415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104095223..104097859-chr14:104105129..104108244,4	K562	blood:
2	chr14:104089914..104092902-chr14:104103042..104105826,2	K562	blood:
3	chr14:104104603..104106806-chr14:104111937..104114817,2	MCF-7	breast:
4	chr14:104093958..104099229-chr14:104101550..104106033,7	K562	blood:
5	chr14:103987449..103989148-chr14:104103898..104105853,2	K562	blood:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction
ENSG00000166165	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10047805	0.89[ASN][1000 genomes]
rs1054080	0.85[ASN][1000 genomes]
rs1078756	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11160754	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11160755	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs11160756	0.80[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1125415	0.81[EUR][1000 genomes]
rs11850979	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12432907	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs12432994	1.00[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12434218	0.90[JPT][hapmap]
rs12435399	0.88[ASN][1000 genomes]
rs12436795	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12586322	0.83[EUR][1000 genomes]
rs12881418	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12889869	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12897511	0.81[ASN][1000 genomes]
rs1799794	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2403203	0.88[ASN][1000 genomes]
rs2896489	0.92[ASN][1000 genomes]
rs3212103	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3212136	1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35015260	0.84[ASN][1000 genomes]
rs35140615	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35469050	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35686878	0.95[ASN][1000 genomes]
rs35918322	0.83[ASN][1000 genomes]
rs3742465	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3759586	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4318144	0.82[ASN][1000 genomes]
rs4561394	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900583	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4900584	0.96[ASN][1000 genomes]
rs4900586	0.82[ASN][1000 genomes]
rs4900587	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4900589	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4906340	0.89[ASN][1000 genomes]
rs4906348	0.87[ASN][1000 genomes]
rs4906349	0.97[ASN][1000 genomes]
rs4906352	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4906355	0.85[ASN][1000 genomes]
rs4906359	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55647815	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61436277	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145234	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7155511	0.82[ASN][1000 genomes]
rs7156832	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729437	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs745079	0.86[JPT][hapmap]
rs8003289	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs8007489	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs8007903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8007915	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs8008451	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs8012775	0.85[ASN][1000 genomes]
rs8018214	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8021368	0.86[JPT][hapmap]
rs861530	0.81[CHB][hapmap]
rs861537	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs861544	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs861545	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs861547	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs8702	1.00[CHB][hapmap];0.91[JPT][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	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	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	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
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7154572	XRCC3	cis	multi-tissue	Pritchard
rs7154572	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs7154572	ZFYVE21	cis	lymphoblastoid	seeQTL
rs7154572	BRF1	cis	parietal	SCAN
rs7154572	XRCC3	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104096600-104118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104097400-104107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:104097400-104107800	Strong transcription	Fetal Stomach	stomach
4	chr14:104097400-104117800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr14:104097400-104119400	Weak transcription	HSMMtube	muscle
6	chr14:104097400-104120000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr14:104097400-104120000	Weak transcription	HUVEC	blood vessel
8	chr14:104097400-104120200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:104097400-104120200	Weak transcription	Colonic Mucosa	Colon
10	chr14:104097400-104120200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:104097400-104120400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:104097400-104120400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:104097600-104106200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:104098600-104119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:104098600-104119800	Weak transcription	K562	blood
18	chr14:104099200-104120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr14:104100000-104119400	Weak transcription	Placenta	Placenta
20	chr14:104101000-104107400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr14:104101000-104120200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr14:104101200-104120600	Weak transcription	Brain Germinal Matrix	brain
23	chr14:104101400-104107400	Weak transcription	Fetal Brain Female	brain
24	chr14:104101600-104119400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr14:104101800-104120800	Weak transcription	Hela-S3	cervix
26	chr14:104102400-104106000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr14:104102600-104111600	Weak transcription	Primary T cells from cord blood	blood
28	chr14:104102600-104120000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr14:104102800-104107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr14:104102800-104118400	Weak transcription	Primary B cells from cord blood	blood
31	chr14:104103000-104119200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr14:104103000-104119400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr14:104103200-104106000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:104104000-104106000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:104104200-104105600	Enhancers	Brain Anterior Caudate	brain
36	chr14:104104200-104105600	Enhancers	Spleen	Spleen
37	chr14:104104200-104105600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr14:104104400-104105600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr14:104104400-104105600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr14:104104400-104105800	Weak transcription	Fetal Intestine Small	intestine
41	chr14:104104400-104107200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr14:104104400-104118000	Weak transcription	A549	lung
43	chr14:104104400-104119400	Weak transcription	Fetal Thymus	thymus
44	chr14:104104600-104106000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr14:104104600-104107400	Weak transcription	GM12878-XiMat	blood
46	chr14:104104600-104107600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr14:104104600-104112400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr14:104104600-104114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr14:104104600-104114800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr14:104104600-104115000	Weak transcription	Fetal Muscle Leg	muscle

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