Variant report

Variant	rs9649860
Chromosome Location	chr7:56110071-56110072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56109516..56112043-chr7:56119039..56120694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146733	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10043	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1064337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238392	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238393	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238395	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11764629	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11765364	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11772545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12535749	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12535872	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12538444	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1894833	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1894834	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2002693	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080141	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2538048	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2908546	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2908547	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2908548	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965455	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55697950	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55863006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56128104	0.81[EUR][1000 genomes]
rs56389944	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62457279	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62457281	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62457282	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62457284	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62457287	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62457288	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62457289	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62457291	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6951202	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6955663	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6965614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140771	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7801405	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7808729	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7811889	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816407	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816410	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8406	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9649860	CHCHD2	cis	multi-tissue	Pritchard
rs9649860	LOC146325	trans	lymphoblastoid	RTeQTL
rs9649860	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56102200-56114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:56102200-56117600	Weak transcription	Gastric	stomach
3	chr7:56102200-56117600	Weak transcription	Spleen	Spleen
4	chr7:56102200-56117800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:56102200-56118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:56102400-56110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:56102400-56114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:56102400-56114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:56102400-56114200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:56102400-56114200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:56102400-56114200	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:56102400-56114200	Weak transcription	Fetal Lung	lung
13	chr7:56102400-56114200	Weak transcription	HUVEC	blood vessel
14	chr7:56102400-56114200	Weak transcription	K562	blood
15	chr7:56102400-56114200	Weak transcription	Osteobl	bone
16	chr7:56102400-56114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:56102400-56117600	Weak transcription	Brain Anterior Caudate	brain
18	chr7:56102400-56117600	Weak transcription	GM12878-XiMat	blood
19	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
20	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
21	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
25	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
26	chr7:56102400-56118000	Weak transcription	NHLF	lung
27	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:56102600-56114200	Weak transcription	HSMM	muscle
29	chr7:56102600-56114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:56102600-56114600	Weak transcription	NH-A	brain
31	chr7:56102600-56114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:56102600-56116200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:56102600-56116400	Weak transcription	HMEC	breast
34	chr7:56102600-56116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:56102600-56117000	Weak transcription	Fetal Brain Female	brain
36	chr7:56102600-56117600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:56102600-56117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:56102600-56117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:56102600-56117800	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:56102600-56118000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:56102600-56118000	Weak transcription	Right Atrium	heart
42	chr7:56102800-56118000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:56102800-56118200	Weak transcription	Primary B cells from cord blood	blood
44	chr7:56102800-56118200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:56103000-56118200	Weak transcription	Thymus	Thymus
46	chr7:56103200-56111600	Weak transcription	HepG2	liver
47	chr7:56107200-56117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:56108000-56117600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:56108000-56117600	Weak transcription	Fetal Brain Male	brain
50	chr7:56108200-56111200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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