Variant report

Variant	rs13244654
Chromosome Location	chr7:56146956-56146957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56132043..56135542-chr7:56146792..56149237,3	K562	blood:
2	chr7:56146012..56147706-chr7:56153751..56155642,2	K562	blood:
3	chr7:56131866..56134691-chr7:56145964..56148262,2	MCF-7	breast:
4	chr7:56140641..56145552-chr7:56146010..56150686,7	K562	blood:
5	chr7:56139442..56142282-chr7:56145954..56148779,2	MCF-7	breast:
6	chr7:56146186..56148845-chr7:56149332..56152482,3	K562	blood:

Variant related genes	Relation type
ENSG00000129103	Chromatin interaction
ENSG00000164776	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10081373	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10258800	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11238394	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11771788	0.92[ASN][1000 genomes]
rs11773374	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11773453	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12537943	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12669623	0.95[ASN][1000 genomes]
rs13234899	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13240915	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs13241866	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs13242830	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1894832	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2002651	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016482	0.81[AMR][1000 genomes]
rs2016724	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2230197	0.91[ASN][1000 genomes]
rs2242508	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs2331180	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2538047	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2908543	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908544	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908545	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908550	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3735665	0.91[ASN][1000 genomes]
rs4049337	0.87[ASN][1000 genomes]
rs4275190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4947534	0.83[CHB][hapmap]
rs4947536	0.81[AMR][1000 genomes]
rs4948102	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4948104	0.95[ASN][1000 genomes]
rs4948106	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62457261	0.83[ASN][1000 genomes]
rs6593297	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6945795	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6954546	0.92[ASN][1000 genomes]
rs6955423	0.84[ASN][1000 genomes]
rs6958480	0.93[ASN][1000 genomes]
rs6966609	0.92[ASN][1000 genomes]
rs766333	0.93[ASN][1000 genomes]
rs7776550	0.82[ASN][1000 genomes]
rs7782243	0.81[AMR][1000 genomes]
rs7783339	0.89[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7793921	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs7799471	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7801169	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs7801467	0.92[ASN][1000 genomes]
rs7811270	0.95[ASN][1000 genomes]
rs7811755	0.83[ASN][1000 genomes]
rs816408	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816409	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816411	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs860118	0.88[CEU][hapmap]
rs933466	0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9767946	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13244654	ZNF713	cis	multi-tissue	Pritchard
rs13244654	CHCHD2	cis	cerebellum	SCAN
rs13244654	SUMF2	cis	parietal	SCAN
rs13244654	CHCHD2	cis	parietal	SCAN
rs13244654	SUMF2	cis	cerebellum	SCAN
rs13244654	GBAS	cis	parietal	SCAN
rs13244654	ZNF713	cis	Liver	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
2	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
3	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
6	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:56139000-56147000	Weak transcription	NH-A	brain
9	chr7:56140400-56152000	Strong transcription	Dnd41	blood
10	chr7:56140800-56153000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:56142000-56151600	Strong transcription	Thymus	Thymus
12	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
13	chr7:56142200-56149600	Weak transcription	Fetal Kidney	kidney
14	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:56142400-56156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:56142600-56159800	Strong transcription	Fetal Intestine Small	intestine
17	chr7:56143400-56150400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:56143800-56151000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:56143800-56153200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:56144000-56147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:56144000-56147000	Strong transcription	Fetal Brain Female	brain
22	chr7:56144000-56147800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:56144000-56148000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:56144000-56151200	Strong transcription	Primary T cells from cord blood	blood
25	chr7:56144200-56147400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:56144200-56147800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr7:56144200-56147800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:56144200-56147800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:56144200-56147800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:56144200-56147800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr7:56144200-56147800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:56144200-56147800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:56144200-56147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:56144200-56147800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr7:56144200-56148000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:56144200-56148800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:56144200-56149800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr7:56144200-56150000	Strong transcription	Fetal Thymus	thymus
39	chr7:56144200-56150400	Strong transcription	A549	lung
40	chr7:56144200-56150800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:56144200-56151800	Strong transcription	Fetal Intestine Large	intestine
42	chr7:56144200-56152000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:56144200-56157200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:56144400-56147000	Strong transcription	Lung	lung
45	chr7:56144400-56147000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr7:56144400-56147000	Strong transcription	NHLF	lung
47	chr7:56144400-56150000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr7:56145200-56150000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:56145200-56151200	Strong transcription	Placenta	Placenta
50	chr7:56145200-56153000	Genic enhancers	Fetal Muscle Leg	muscle

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