Variant report

Variant	rs61791721
Chromosome Location	chr3:135804550-135804551
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	chr3:135803875..135806312-chr3:135914228..135916127,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1154988	0.81[EUR][1000 genomes]
rs34330586	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34894639	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772390	0.91[ASN][1000 genomes]
rs4431046	0.82[AFR][1000 genomes]
rs4678322	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678361	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61791757	0.87[EUR][1000 genomes]
rs645040	0.82[EUR][1000 genomes]
rs6779146	0.85[EUR][1000 genomes]
rs687339	0.83[EUR][1000 genomes]
rs9840812	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9865841	0.88[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak 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 target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61791721	PDCD6	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135771200-135809600	Weak transcription	Gastric	stomach
2	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
3	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:135784200-135805600	Weak transcription	Stomach Mucosa	stomach
5	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
6	chr3:135790600-135809600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:135790800-135807000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:135790800-135809400	Weak transcription	Adipose Nuclei	Adipose
9	chr3:135790800-135809600	Weak transcription	Aorta	Aorta
10	chr3:135790800-135809600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:135790800-135809600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:135790800-135809600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:135790800-135809600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:135794400-135806600	Weak transcription	Fetal Heart	heart
15	chr3:135794400-135809600	Weak transcription	NH-A	brain
16	chr3:135798200-135809400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:135798600-135804600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:135798600-135805800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:135799600-135806600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:135800000-135805200	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:135800000-135805600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:135800400-135808000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:135800400-135815400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:135800600-135808400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:135800800-135805000	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:135801000-135804600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr3:135801600-135805000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:135801800-135804600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr3:135801800-135804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:135801800-135805200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:135801800-135805400	Strong transcription	Ovary	ovary
32	chr3:135802200-135809000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:135802400-135804600	Weak transcription	Left Ventricle	heart
34	chr3:135802400-135804600	Weak transcription	NHDF-Ad	bronchial
35	chr3:135802400-135806800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:135802600-135805000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:135802600-135809800	Weak transcription	Placenta	Placenta
38	chr3:135802800-135807000	Weak transcription	Fetal Kidney	kidney
39	chr3:135803000-135826600	Weak transcription	Liver	Liver
40	chr3:135803200-135809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:135803200-135809600	Weak transcription	Pancreas	Pancrea
42	chr3:135803200-135809600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:135803600-135804800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:135803600-135806800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:135803600-135806800	Weak transcription	Fetal Brain Female	brain
47	chr3:135803600-135807200	Strong transcription	Fetal Stomach	stomach
48	chr3:135803600-135809400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:135803600-135809400	Weak transcription	HSMMtube	muscle
50	chr3:135803600-135809600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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