Variant report

Variant	rs823530
Chromosome Location	chr3:195182985-195182986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195167466..195170078-chr3:195181038..195183808,2	MCF-7	breast:
2	chr3:195161338..195166819-chr3:195177986..195183968,7	K562	blood:
3	chr3:195161787..195165604-chr3:195180533..195183968,4	K562	blood:

Variant related genes	Relation type
ENSG00000114331	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11927933	0.86[EUR][1000 genomes]
rs2641372	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28688106	0.83[EUR][1000 genomes]
rs752206	0.91[CHB][hapmap]
rs823528	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs823531	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs823533	0.83[EUR][1000 genomes]
rs823534	0.83[EUR][1000 genomes]
rs823536	0.83[EUR][1000 genomes]
rs862066	0.83[EUR][1000 genomes]
rs9837749	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
6	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
7	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
10	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
11	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
12	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
13	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
15	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
17	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv4181	chr3:195171990-195216923	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv1845367	chr3:195175217-195486486	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs823530	ACAP2	cis	parietal	SCAN
rs823530	LOC401109	cis	parietal	SCAN
rs823530	PIGX	cis	cerebellum	SCAN
rs823530	RAI14	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195180400-195189000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:195182200-195183200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:195182200-195183200	Enhancers	Duodenum Mucosa	Duodenum
4	chr3:195182200-195183400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:195182400-195183000	Enhancers	Brain Hippocampus Middle	brain
6	chr3:195182400-195183000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:195182400-195183000	Enhancers	Esophagus	oesophagus
8	chr3:195182400-195183000	Enhancers	Fetal Muscle Trunk	muscle
9	chr3:195182400-195183000	Enhancers	Left Ventricle	heart
10	chr3:195182400-195183000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
11	chr3:195182400-195183000	Flanking Active TSS	HSMMtube	muscle
12	chr3:195182400-195183200	Enhancers	Fetal Kidney	kidney
13	chr3:195182400-195183200	Enhancers	Fetal Muscle Leg	muscle
14	chr3:195182400-195183200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr3:195182400-195183200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:195182400-195183200	Enhancers	HSMM	muscle
17	chr3:195182400-195183200	Enhancers	K562	blood
18	chr3:195182400-195183400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr3:195182600-195183000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:195182600-195183000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:195182600-195183000	Enhancers	Brain Angular Gyrus	brain
22	chr3:195182600-195183000	Enhancers	Brain Anterior Caudate	brain
23	chr3:195182600-195183000	Enhancers	Colonic Mucosa	Colon
24	chr3:195182600-195183000	Enhancers	Lung	lung
25	chr3:195182600-195183200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
26	chr3:195182600-195183200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:195182600-195183200	Enhancers	NH-A	brain
28	chr3:195182600-195194800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:195182800-195183000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:195182800-195183000	Enhancers	Fetal Heart	heart
31	chr3:195182800-195183200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:195182800-195183200	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:195182800-195183800	Weak transcription	Ovary	ovary
34	chr3:195182800-195184000	Enhancers	Stomach Mucosa	stomach

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