Variant report

Variant	rs16843661
Chromosome Location	chr3:135756999-135757000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135744654..135746956-chr3:135755172..135758083,2	MCF-7	breast:
2	chr3:135637277..135640102-chr3:135755652..135757448,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11918906	1.00[EUR][1000 genomes]
rs11925256	1.00[EUR][1000 genomes]
rs16843565	1.00[EUR][1000 genomes]
rs16843571	1.00[EUR][1000 genomes]
rs16843592	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16843633	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56736462	1.00[AFR][1000 genomes]
rs57374999	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58030391	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58096685	1.00[AFR][1000 genomes]
rs58503058	1.00[AFR][1000 genomes]
rs59720283	1.00[AFR][1000 genomes]
rs59985749	1.00[AFR][1000 genomes]
rs60165730	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60393211	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60707425	0.88[AFR][1000 genomes]
rs61209689	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979686	1.00[EUR][1000 genomes]
rs72979693	1.00[EUR][1000 genomes]
rs72979696	1.00[EUR][1000 genomes]
rs72979701	1.00[EUR][1000 genomes]
rs72981415	1.00[AFR][1000 genomes]
rs72981481	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72981494	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72983403	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72983409	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72983437	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72983449	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72983460	1.00[EUR][1000 genomes]
rs72983474	1.00[AFR][1000 genomes]
rs72983475	1.00[AFR][1000 genomes]
rs72983479	1.00[AFR][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	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	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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:135726400-135758400	Weak transcription	Lung	lung
3	chr3:135727400-135760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:135735800-135760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:135738000-135758400	Weak transcription	Gastric	stomach
7	chr3:135738000-135761200	Weak transcription	Fetal Brain Male	brain
8	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:135738400-135763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:135738400-135763600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:135739800-135767800	Weak transcription	NHDF-Ad	bronchial
12	chr3:135741000-135763600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:135741800-135759800	Weak transcription	Placenta	Placenta
14	chr3:135742000-135763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:135742000-135763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:135742200-135763600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:135742200-135763600	Weak transcription	NHEK	skin
18	chr3:135742800-135774200	Weak transcription	HMEC	breast
19	chr3:135744200-135763600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:135746400-135763600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:135746600-135761000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:135747000-135757400	Weak transcription	Right Ventricle	heart
24	chr3:135747600-135760600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:135747800-135763600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:135748400-135757800	Weak transcription	Aorta	Aorta
27	chr3:135748400-135762400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:135748400-135763000	Weak transcription	NH-A	brain
29	chr3:135748400-135763200	Weak transcription	Fetal Intestine Large	intestine
30	chr3:135748400-135763200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:135748400-135763400	Weak transcription	HSMMtube	muscle
32	chr3:135748400-135763600	Weak transcription	Colonic Mucosa	Colon
33	chr3:135748400-135763800	Weak transcription	NHLF	lung
34	chr3:135748600-135757400	Weak transcription	Adipose Nuclei	Adipose
35	chr3:135748600-135763000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:135748600-135763200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:135748600-135763200	Weak transcription	Esophagus	oesophagus
38	chr3:135748800-135760200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:135749000-135757400	Weak transcription	Fetal Stomach	stomach
40	chr3:135749000-135759600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:135749000-135763200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:135749000-135763600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:135749000-135763600	Weak transcription	Pancreas	Pancrea
44	chr3:135749400-135757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:135749400-135763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:135749800-135760200	Weak transcription	Ovary	ovary
47	chr3:135750000-135757200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:135750200-135763600	Weak transcription	Fetal Lung	lung
49	chr3:135750400-135760800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:135750400-135772800	Weak transcription	Brain Substantia Nigra	brain

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