Variant report

Variant	rs16843653
Chromosome Location	chr3:135747416-135747417
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135682268..135685211-chr3:135746856..135748620,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512973	0.81[YRI][hapmap]
rs16843557	1.00[AMR][1000 genomes]
rs6769336	0.88[AFR][1000 genomes]
rs6772597	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773511	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6783238	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6807844	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16843653	TFEC	trans	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
2	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:135726200-135748000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:135726400-135758400	Weak transcription	Lung	lung
5	chr3:135727400-135760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:135728000-135748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:135735800-135760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:135738000-135750000	Weak transcription	Brain Substantia Nigra	brain
10	chr3:135738000-135758400	Weak transcription	Gastric	stomach
11	chr3:135738000-135761200	Weak transcription	Fetal Brain Male	brain
12	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:135738200-135749600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:135738400-135763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:135738400-135763600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:135739800-135767800	Weak transcription	NHDF-Ad	bronchial
17	chr3:135741000-135763600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:135741800-135748000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:135741800-135748000	Weak transcription	Esophagus	oesophagus
20	chr3:135741800-135748000	Weak transcription	Osteobl	bone
21	chr3:135741800-135750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:135741800-135759800	Weak transcription	Placenta	Placenta
23	chr3:135742000-135747800	Weak transcription	Aorta	Aorta
24	chr3:135742000-135748000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:135742000-135763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:135742000-135763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:135742200-135748000	Weak transcription	Brain Germinal Matrix	brain
28	chr3:135742200-135763600	Weak transcription	Fetal Intestine Small	intestine
29	chr3:135742200-135763600	Weak transcription	NHEK	skin
30	chr3:135742800-135774200	Weak transcription	HMEC	breast
31	chr3:135743000-135755600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:135743200-135748000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:135744200-135763600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:135745000-135751200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:135745200-135748000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:135745200-135750200	Weak transcription	Brain Anterior Caudate	brain
37	chr3:135745600-135748600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:135745600-135750000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:135745600-135751200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:135745800-135747800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:135745800-135748800	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:135745800-135749000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:135745800-135749000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:135745800-135750000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:135745800-135755200	Weak transcription	Psoas Muscle	Psoas
46	chr3:135746000-135747600	Strong transcription	HSMM	muscle
47	chr3:135746000-135748400	Strong transcription	NH-A	brain
48	chr3:135746000-135748800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:135746000-135748800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:135746000-135750600	Weak transcription	Liver	Liver

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