Variant report

Variant	rs248330
Chromosome Location	chr5:179375727-179375728
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	chr5:179372183..179374228-chr5:179375426..179378346,2	MCF-7	breast:
2	chr5:179228575..179230417-chr5:179374164..179376318,2	K562	blood:

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs155575	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs155576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155577	0.88[CEU][hapmap]
rs190328	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248321	0.84[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs248322	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248327	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248328	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248329	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27011	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs36750	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs389849	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67542237	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705448	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs248330	ZNF346	cis	parietal	SCAN
rs248330	LOC202181	cis	parietal	SCAN
rs248330	CANX	cis	parietal	SCAN
rs248330	PDLIM7	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
2	chr5:179347200-179381000	Weak transcription	Brain Angular Gyrus	brain
3	chr5:179354200-179381400	Weak transcription	Fetal Brain Female	brain
4	chr5:179359000-179381000	Weak transcription	Brain Substantia Nigra	brain
5	chr5:179359000-179381200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:179360200-179377400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:179366600-179382000	Weak transcription	Fetal Lung	lung
8	chr5:179367400-179381400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:179368400-179381400	Weak transcription	Left Ventricle	heart
10	chr5:179369000-179381000	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:179369000-179381400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:179369800-179381400	Weak transcription	Ovary	ovary
13	chr5:179370000-179382800	Weak transcription	Lung	lung
14	chr5:179370200-179392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:179370400-179376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:179370800-179380800	Weak transcription	Adipose Nuclei	Adipose
17	chr5:179370800-179386800	Weak transcription	HepG2	liver
18	chr5:179371000-179381400	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:179371800-179377400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:179372000-179381000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:179372200-179376200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:179372200-179381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:179372200-179386800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:179372400-179382000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:179372800-179381800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:179372800-179382000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:179373000-179381200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:179373000-179382000	Weak transcription	Aorta	Aorta
29	chr5:179373000-179382000	Weak transcription	Gastric	stomach
30	chr5:179373000-179382800	Weak transcription	Brain Anterior Caudate	brain
31	chr5:179373000-179389600	Weak transcription	Fetal Intestine Large	intestine
32	chr5:179373200-179381400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:179373200-179381600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:179373200-179381800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:179373200-179382000	Weak transcription	Right Ventricle	heart
36	chr5:179373200-179382200	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:179373200-179383000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:179373400-179381000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:179373400-179381000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:179373400-179381600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:179373400-179400600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:179373800-179378600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:179373800-179401600	Weak transcription	Colonic Mucosa	Colon
44	chr5:179374000-179386000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:179374600-179381400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:179374600-179382000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179374600-179387200	Weak transcription	HSMMtube	muscle
48	chr5:179374600-179387400	Weak transcription	Pancreas	Pancrea
49	chr5:179374800-179379000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:179375000-179375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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