Variant report

Variant	rs6966609
Chromosome Location	chr7:56158739-56158740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56158093-56158964	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56153270..56156192-chr7:56157792..56160758,3	K562	blood:
2	chr7:56158331..56162402-chr7:56164304..56169225,5	K562	blood:

Variant related genes	Relation type
PHKG1	TF binding region
ENSG00000164776	Chromatin interaction
ENSG00000238673	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10081373	0.93[ASN][1000 genomes]
rs10255049	0.84[AMR][1000 genomes]
rs11771788	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537943	0.96[ASN][1000 genomes]
rs12669623	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13240915	0.84[ASN][1000 genomes]
rs13241866	0.84[ASN][1000 genomes]
rs13244654	0.92[ASN][1000 genomes]
rs2002651	0.89[ASN][1000 genomes]
rs2016724	0.87[ASN][1000 genomes]
rs2230197	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242508	0.93[ASN][1000 genomes]
rs2538047	0.93[ASN][1000 genomes]
rs3735665	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4049337	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4275190	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4948102	0.84[ASN][1000 genomes]
rs4948104	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593297	0.83[AMR][1000 genomes]
rs6954546	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955423	0.84[ASN][1000 genomes]
rs6958480	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766333	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776550	0.81[ASN][1000 genomes]
rs7793921	0.84[AMR][1000 genomes]
rs7801467	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811270	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811755	0.83[ASN][1000 genomes]
rs9767946	0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6966609	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
3	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
5	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:56142600-56159800	Strong transcription	Fetal Intestine Small	intestine
7	chr7:56146000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:56147000-56167400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:56147400-56167000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:56147400-56169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:56147600-56160400	Weak transcription	Fetal Brain Male	brain
12	chr7:56147600-56167200	Weak transcription	HMEC	breast
13	chr7:56147600-56167400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:56147800-56159600	Weak transcription	NHDF-Ad	bronchial
15	chr7:56147800-56160200	Weak transcription	HSMM	muscle
16	chr7:56147800-56160600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:56147800-56160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:56147800-56164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:56147800-56167200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr7:56147800-56167400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:56148000-56165600	Weak transcription	Primary B cells from cord blood	blood
22	chr7:56148000-56167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:56148800-56167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:56149600-56167200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:56149800-56167600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:56149800-56168000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:56150000-56164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:56150000-56166200	Weak transcription	Fetal Thymus	thymus
29	chr7:56150000-56166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:56150200-56160600	Weak transcription	NHEK	skin
31	chr7:56150400-56164000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:56150600-56159600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:56150800-56160400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:56151200-56159200	Weak transcription	Fetal Lung	lung
35	chr7:56151400-56159600	Weak transcription	Brain Angular Gyrus	brain
36	chr7:56151400-56160200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:56151400-56160400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:56151600-56159400	Strong transcription	Fetal Stomach	stomach
39	chr7:56151800-56159600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:56152000-56167400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:56152200-56159400	Weak transcription	HSMMtube	muscle
42	chr7:56153600-56159600	Weak transcription	Osteobl	bone
43	chr7:56154600-56160200	Weak transcription	Liver	Liver
44	chr7:56155400-56159200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:56155400-56159400	Weak transcription	Ovary	ovary
46	chr7:56155400-56160400	Weak transcription	Lung	lung
47	chr7:56155600-56159400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:56155600-56159600	Weak transcription	Aorta	Aorta
49	chr7:56155600-56159600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:56155600-56159600	Weak transcription	Colonic Mucosa	Colon

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