Variant report

Variant	rs6947109
Chromosome Location	chr7:56049720-56049721
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	chr7:56047807..56050319-chr7:56171893..56174174,2	K562	blood:

Variant related genes	Relation type
ENSG00000106153	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17172508	1.00[ASN][1000 genomes]
rs17664478	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3966180	1.00[ASN][1000 genomes]
rs4443615	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4495378	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4948095	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4948098	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948103	1.00[ASN][1000 genomes]
rs4948107	1.00[ASN][1000 genomes]
rs4948108	1.00[ASN][1000 genomes]
rs58571234	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59193297	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59852874	1.00[ASN][1000 genomes]
rs6593298	1.00[ASN][1000 genomes]
rs66485869	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66741911	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67818657	1.00[ASN][1000 genomes]
rs6954669	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6964563	0.83[AFR][1000 genomes]
rs73132850	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73132884	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73132888	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73134793	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73134796	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73138732	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138750	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140778	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779821	1.00[ASN][1000 genomes]
rs7784730	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791221	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806994	0.81[EUR][1000 genomes]
rs7808487	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810142	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6947109	CHCHD2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:56039200-56081600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:56039400-56062400	Weak transcription	Stomach Mucosa	stomach
7	chr7:56043800-56049800	Strong transcription	Primary B cells from cord blood	blood
8	chr7:56044000-56053200	Strong transcription	Primary T cells from cord blood	blood
9	chr7:56044600-56050600	Weak transcription	Psoas Muscle	Psoas
10	chr7:56045000-56067400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:56045200-56068200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:56045400-56049800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:56045400-56050000	Strong transcription	Hela-S3	cervix
14	chr7:56045400-56051600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:56045400-56054000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr7:56045400-56054000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr7:56045400-56055000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:56045400-56057400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:56045400-56057400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:56045400-56057600	Strong transcription	Dnd41	blood
21	chr7:56045400-56059200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:56045400-56067000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:56045400-56067000	Strong transcription	Liver	Liver
24	chr7:56045400-56067200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:56045400-56067400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:56045600-56049800	Strong transcription	Aorta	Aorta
27	chr7:56045600-56051200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:56045600-56051600	Strong transcription	HepG2	liver
29	chr7:56045600-56053000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr7:56045600-56053200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:56045600-56053600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr7:56045600-56053800	Strong transcription	Left Ventricle	heart
33	chr7:56045600-56054000	Strong transcription	Placenta	Placenta
34	chr7:56045600-56054400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:56045600-56054400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr7:56045600-56056400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:56045600-56056800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:56045600-56057400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:56045600-56057600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:56045600-56062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:56045600-56066600	Strong transcription	Fetal Stomach	stomach
42	chr7:56045600-56067400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:56045600-56067400	Strong transcription	Fetal Intestine Large	intestine
44	chr7:56045800-56050000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:56045800-56050600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:56045800-56051600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:56045800-56053200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr7:56045800-56053400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:56045800-56053800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:56045800-56054400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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