Variant report

Variant	rs11629561
Chromosome Location	chr15:78438122-78438123
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78436066..78438607-chr15:78439895..78441680,2	K562	blood:
2	chr15:78437153..78440009-chr15:78444178..78446804,3	MCF-7	breast:
3	chr15:78437349..78439944-chr15:78555293..78556889,2	MCF-7	breast:
4	chr15:78437651..78440580-chr15:78459542..78461046,2	MCF-7	breast:
5	chr15:78437413..78439918-chr15:78471623..78473708,2	K562	blood:
6	chr15:78426055..78428346-chr15:78436183..78438129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103740	Chromatin interaction
ENSG00000259708	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11630776	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631100	0.84[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631653	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11634325	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638921	0.86[EUR][1000 genomes]
rs12904404	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904688	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904700	0.86[EUR][1000 genomes]
rs12906189	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912695	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478430	1.00[JPT][hapmap]
rs1982241	0.87[EUR][1000 genomes]
rs2011323	1.00[JPT][hapmap]
rs2044098	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304825	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2868607	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087998	0.87[ASN][1000 genomes]
rs3816253	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs8035724	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11629561	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78424600-78440800	Weak transcription	HSMMtube	muscle
2	chr15:78425000-78440600	Weak transcription	Fetal Stomach	stomach
3	chr15:78426000-78440200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:78427200-78438600	Weak transcription	Placenta	Placenta
5	chr15:78427200-78439200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:78432600-78440200	Weak transcription	Small Intestine	intestine
7	chr15:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:78433600-78440400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:78433800-78440200	Weak transcription	Right Ventricle	heart
10	chr15:78434000-78439800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:78434800-78439200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:78435200-78438600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:78435200-78438800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:78435200-78438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:78435200-78440400	Weak transcription	HepG2	liver
16	chr15:78435400-78438400	Weak transcription	Fetal Intestine Large	intestine
17	chr15:78435400-78438400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:78436000-78440600	Weak transcription	Thymus	Thymus
19	chr15:78437000-78440000	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:78437600-78438400	Weak transcription	Adipose Nuclei	Adipose
21	chr15:78437600-78440600	Weak transcription	HSMM	muscle

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