Variant report

Variant	rs62457286
Chromosome Location	chr7:56144656-56144657
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	chr7:56131320..56133312-chr7:56141582..56144695,3	MCF-7	breast:
2	chr7:56130207..56133425-chr7:56142360..56145052,4	K562	blood:

Variant related genes	Relation type
ENSG00000146731	Chromatin interaction
ENSG00000129103	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10043	0.82[ASN][1000 genomes]
rs11238392	0.82[ASN][1000 genomes]
rs11238393	0.82[ASN][1000 genomes]
rs11764629	0.82[ASN][1000 genomes]
rs11765364	0.82[ASN][1000 genomes]
rs12535749	0.82[ASN][1000 genomes]
rs12535872	0.82[ASN][1000 genomes]
rs12538444	0.82[ASN][1000 genomes]
rs2080141	0.82[ASN][1000 genomes]
rs2538048	0.82[ASN][1000 genomes]
rs2908546	0.82[ASN][1000 genomes]
rs2908547	0.82[ASN][1000 genomes]
rs55697950	0.82[ASN][1000 genomes]
rs56389944	0.82[ASN][1000 genomes]
rs62457279	0.82[ASN][1000 genomes]
rs62457281	0.82[ASN][1000 genomes]
rs62457282	0.82[ASN][1000 genomes]
rs62457284	0.82[ASN][1000 genomes]
rs62457287	0.82[ASN][1000 genomes]
rs62457288	0.82[ASN][1000 genomes]
rs62457289	0.82[ASN][1000 genomes]
rs6951202	0.82[ASN][1000 genomes]
rs7808729	0.82[ASN][1000 genomes]
rs7811889	0.82[ASN][1000 genomes]
rs816407	0.82[ASN][1000 genomes]
rs8406	0.82[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
rs62457286	PSPH,LOC389493	cis	brain	BrainEAC
rs62457286	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs62457286	LOC146325	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
3	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
6	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
7	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:56133600-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
12	chr7:56137200-56146000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:56138800-56146800	Weak transcription	Aorta	Aorta
14	chr7:56138800-56146800	Weak transcription	HSMMtube	muscle
15	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:56139000-56145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:56139000-56145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:56139000-56145600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:56139000-56146800	Weak transcription	HSMM	muscle
21	chr7:56139000-56147000	Weak transcription	NH-A	brain
22	chr7:56139200-56146400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:56139400-56146000	Weak transcription	Primary B cells from cord blood	blood
24	chr7:56139400-56146000	Weak transcription	Brain Angular Gyrus	brain
25	chr7:56140400-56152000	Strong transcription	Dnd41	blood
26	chr7:56140800-56153000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:56141000-56145600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:56141000-56145800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:56141000-56145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:56142000-56145600	Weak transcription	K562	blood
31	chr7:56142000-56151600	Strong transcription	Thymus	Thymus
32	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
33	chr7:56142200-56145600	Weak transcription	Brain Germinal Matrix	brain
34	chr7:56142200-56149600	Weak transcription	Fetal Kidney	kidney
35	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:56142400-56145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:56142400-56145600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:56142400-56145800	Weak transcription	Gastric	stomach
39	chr7:56142400-56146200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:56142400-56146200	Weak transcription	HepG2	liver
41	chr7:56142400-56146600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:56142400-56156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:56142600-56145200	Weak transcription	Placenta	Placenta
44	chr7:56142600-56145400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:56142600-56145400	Weak transcription	Osteobl	bone
46	chr7:56142600-56145600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:56142600-56145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr7:56142600-56145800	Weak transcription	Adipose Nuclei	Adipose
49	chr7:56142600-56145800	Weak transcription	Brain Anterior Caudate	brain
50	chr7:56142600-56145800	Weak transcription	Colonic Mucosa	Colon

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