Variant report

Variant	rs13412567
Chromosome Location	chr2:110457214-110457215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:110251030..110252990-chr2:110456796..110459130,2	MCF-7	breast:
2	chr2:110448860..110451587-chr2:110455006..110457237,2	MCF-7	breast:
3	chr2:110455483..110458569-chr2:110458609..110461502,6	MCF-7	breast:
4	chr2:110456223..110458678-chr2:110473323..110476138,2	MCF-7	breast:
5	chr2:110448146..110451787-chr2:110456949..110458921,3	MCF-7	breast:
6	chr2:110371478..110373330-chr2:110455377..110458240,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10178717	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10185743	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11240785	1.00[ASN][1000 genomes]
rs13386685	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13389531	0.83[AFR][1000 genomes]
rs13401439	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs951954	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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	60 gene(s)	inside rSNPs	diseases
3	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv999552	chr2:110396395-110978224	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv428061	chr2:110423940-110714002	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv2751812	chr2:110457214-110980346	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13412567	CCDC37	trans	brain	seeQTL
rs13412567	CAPS	trans	brain	seeQTL
rs13412567	DYNLRB2	trans	brain	seeQTL
rs13412567	ZMYND10	trans	brain	seeQTL
rs13412567	CCDC11	trans	brain	seeQTL
rs13412567	C1orf87	trans	brain	seeQTL
rs13412567	C1orf194	trans	brain	seeQTL
rs13412567	EFCAB1	trans	brain	seeQTL
rs13412567	SLC47A2	trans	brain	seeQTL
rs13412567	CCDC19	trans	brain	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110451000-110458000	Weak transcription	Spleen	Spleen
2	chr2:110453200-110458000	Weak transcription	Esophagus	oesophagus
3	chr2:110453400-110457800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:110455400-110461800	Enhancers	Placenta	Placenta
5	chr2:110455800-110461600	Enhancers	Fetal Intestine Small	intestine
6	chr2:110456200-110458600	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr2:110456200-110459200	Enhancers	Hela-S3	cervix
8	chr2:110456400-110457400	Enhancers	Ovary	ovary
9	chr2:110456400-110457600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:110456400-110457600	Enhancers	Left Ventricle	heart
11	chr2:110456400-110458600	Enhancers	Colon Smooth Muscle	Colon
12	chr2:110456400-110458600	Enhancers	Fetal Muscle Leg	muscle
13	chr2:110456400-110458800	Enhancers	Fetal Heart	heart
14	chr2:110456400-110459200	Enhancers	HMEC	breast
15	chr2:110456400-110460200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:110456400-110460200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:110456400-110460200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:110456400-110460400	Enhancers	Stomach Mucosa	stomach
19	chr2:110456400-110461000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:110456400-110461800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:110456600-110457400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr2:110456600-110457400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:110456600-110457400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:110456600-110457600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr2:110456600-110457600	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr2:110456600-110457600	Flanking Active TSS	NHEK	skin
27	chr2:110456600-110457600	Enhancers	Osteobl	bone
28	chr2:110456600-110457800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:110456600-110457800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:110456600-110458200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:110456600-110458800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:110456600-110458800	Enhancers	Right Atrium	heart
33	chr2:110456600-110459000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:110456600-110459000	Enhancers	Fetal Stomach	stomach
35	chr2:110456600-110459000	Enhancers	Pancreas	Pancrea
36	chr2:110456600-110459600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:110456600-110459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:110456600-110460000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:110456600-110460200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:110456600-110460200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:110456600-110460200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:110456600-110461400	Enhancers	Fetal Lung	lung
43	chr2:110456600-110462000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:110456800-110457400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:110456800-110457400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:110456800-110457400	Enhancers	Right Ventricle	heart
47	chr2:110456800-110457400	Enhancers	HUVEC	blood vessel
48	chr2:110456800-110457600	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:110456800-110457600	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr2:110456800-110457600	Flanking Active TSS	NH-A	brain

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