Variant report

Variant	rs12935422
Chromosome Location	chr16:71664225-71664226
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71658952..71666464-chr16:71755738..71760832,8	MCF-7	breast:
2	chr16:71572964..71574516-chr16:71664027..71666330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10500562	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12149264	0.81[EUR][1000 genomes]
rs12444890	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12447672	0.84[AFR][1000 genomes]
rs12923781	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12924650	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12927768	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12931191	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17282500	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17354693	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17356206	0.84[AFR][1000 genomes]
rs34381861	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs35538253	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71403859	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8063455	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12935422	RP11-432I5.1	cis	Thyroid	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71661000-71671000	Weak transcription	Right Atrium	heart
2	chr16:71661000-71674200	Weak transcription	Gastric	stomach
3	chr16:71661200-71667000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr16:71662000-71674200	Weak transcription	Lung	lung
6	chr16:71662200-71665600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:71662800-71673600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr16:71663000-71666200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr16:71663000-71669600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr16:71663000-71670800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:71663200-71664600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:71663200-71664600	Weak transcription	HMEC	breast
15	chr16:71663200-71666000	Weak transcription	Fetal Heart	heart
16	chr16:71663200-71666400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:71663200-71668600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr16:71663200-71670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:71663200-71670600	Weak transcription	Osteobl	bone
20	chr16:71663200-71670800	Weak transcription	Ovary	ovary
21	chr16:71663200-71671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:71663200-71673800	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:71663200-71676800	Weak transcription	Fetal Kidney	kidney
24	chr16:71663400-71664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:71663400-71665800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr16:71663400-71668200	Weak transcription	Fetal Stomach	stomach
27	chr16:71663400-71668800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr16:71663400-71669200	Strong transcription	Fetal Intestine Small	intestine
29	chr16:71663400-71669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr16:71663400-71670000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr16:71663400-71674200	Weak transcription	Adipose Nuclei	Adipose
32	chr16:71663400-71674200	Weak transcription	Aorta	Aorta
33	chr16:71663400-71674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:71663400-71674400	Weak transcription	Esophagus	oesophagus
35	chr16:71663400-71678400	Weak transcription	Fetal Lung	lung
36	chr16:71663600-71665200	Strong transcription	Liver	Liver
37	chr16:71663600-71668000	Weak transcription	Colonic Mucosa	Colon
38	chr16:71663600-71668600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr16:71663600-71686600	Weak transcription	Small Intestine	intestine
40	chr16:71663800-71664600	Strong transcription	Fetal Intestine Large	intestine
41	chr16:71663800-71665400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr16:71663800-71667000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr16:71663800-71667800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr16:71663800-71667800	Weak transcription	Pancreas	Pancrea
45	chr16:71663800-71669800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr16:71663800-71673800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr16:71663800-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr16:71663800-71680600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr16:71663800-71681400	Weak transcription	Left Ventricle	heart
50	chr16:71663800-71681400	Weak transcription	HepG2	liver

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