Variant report

Variant	rs11238386
Chromosome Location	chr7:56033141-56033142
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56032893..56034835-chr7:56039528..56041569,2	K562	blood:
2	chr7:56018437..56023114-chr7:56029023..56035214,11	K562	blood:
3	chr7:56017138..56022365-chr7:56030961..56033857,7	MCF-7	breast:
4	chr7:56029925..56033959-chr7:56116899..56121286,8	MCF-7	breast:
5	chr7:55638686..55640788-chr7:56032408..56034180,2	K562	blood:
6	chr7:56031349..56034408-chr7:56116793..56119463,3	K562	blood:
7	chr7:56017145..56021503-chr7:56030472..56033942,8	MCF-7	breast:
8	chr7:56031249..56033824-chr7:56141998..56144238,2	MCF-7	breast:
9	chr7:56031887..56033611-chr7:56046548..56048449,2	K562	blood:
10	chr7:56031975..56033890-chr7:56117908..56119685,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000146729	Chromatin interaction
ENSG00000154978	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000239789	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10237524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226516	0.82[CHD][hapmap]
rs13245637	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34929372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160834	0.81[AFR][1000 genomes]
rs4255090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	esv3415140	chr7:56031258-56033556	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11238386	ZNF479	cis	cerebellum	SCAN
rs11238386	ZNF713	cis	cerebellum	SCAN
rs11238386	CHCHD2	cis	parietal	SCAN
rs11238386	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs11238386	CHCHD2	cis	cerebellum	SCAN
rs11238386	ZNF713	cis	parietal	SCAN
rs11238386	GBAS	cis	multi-tissue	Pritchard
rs11238386	LOC146325	trans	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56031400-56033800	Active TSS	Fetal Kidney	kidney
2	chr7:56031600-56033200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:56031600-56033600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:56031600-56033800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr7:56031800-56033200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:56031800-56033200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:56031800-56033200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:56031800-56033200	Active TSS	Aorta	Aorta
9	chr7:56031800-56033200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:56031800-56033200	Active TSS	Brain Substantia Nigra	brain
11	chr7:56031800-56033200	Active TSS	Ovary	ovary
12	chr7:56031800-56033400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:56031800-56033400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:56031800-56033400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr7:56031800-56033400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:56031800-56033400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr7:56031800-56033400	Active TSS	Fetal Intestine Large	intestine
18	chr7:56031800-56033400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr7:56031800-56033600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr7:56031800-56033600	Active TSS	Brain Anterior Caudate	brain
21	chr7:56031800-56033600	Active TSS	Colon Smooth Muscle	Colon
22	chr7:56031800-56033600	Active TSS	A549	lung
23	chr7:56031800-56033600	Active TSS	Hela-S3	cervix
24	chr7:56031800-56033800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr7:56031800-56033800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr7:56031800-56033800	Active TSS	HSMMtube	muscle
27	chr7:56031800-56033800	Active TSS	NHLF	lung
28	chr7:56031800-56034400	Active TSS	Left Ventricle	heart
29	chr7:56031800-56034600	Active TSS	Right Ventricle	heart
30	chr7:56032000-56033200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:56032000-56033200	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr7:56032000-56033200	Active TSS	Duodenum Mucosa	Duodenum
33	chr7:56032000-56033200	Active TSS	Fetal Muscle Leg	muscle
34	chr7:56032000-56033200	Active TSS	Placenta	Placenta
35	chr7:56032000-56033400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr7:56032000-56033400	Active TSS	Small Intestine	intestine
37	chr7:56032000-56033400	Active TSS	Stomach Smooth Muscle	stomach
38	chr7:56032000-56033400	Active TSS	GM12878-XiMat	blood
39	chr7:56032000-56033400	Active TSS	HepG2	liver
40	chr7:56032000-56033400	Active TSS	HMEC	breast
41	chr7:56032000-56033400	Active TSS	HUVEC	blood vessel
42	chr7:56032000-56033600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr7:56032000-56033600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:56032000-56033600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr7:56032000-56033600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:56032000-56033600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:56032000-56033600	Active TSS	Brain Cingulate Gyrus	brain
48	chr7:56032000-56033600	Active TSS	Rectal Smooth Muscle	rectum
49	chr7:56032000-56033800	Active TSS	Psoas Muscle	Psoas
50	chr7:56032000-56034000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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