Variant report

Variant	rs16846346
Chromosome Location	chr1:226838508-226838509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226836884..226839158-chr1:226845149..226848067,3	K562	blood:
2	chr1:226838115..226840553-chr1:226843836..226846958,3	MCF-7	breast:
3	chr1:226837244..226840102-chr1:226865021..226866969,2	MCF-7	breast:
4	chr1:226829138..226831171-chr1:226838507..226841235,2	MCF-7	breast:
5	chr1:226832724..226834932-chr1:226836674..226839333,2	MCF-7	breast:
6	chr1:226837983..226838607-chr1:226896830..226897365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12076436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12739464	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738722	0.81[AMR][1000 genomes]
rs3754378	0.81[AMR][1000 genomes];0.81[EUR][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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3437235	chr1:226835029-226839227	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
2	chr1:226820400-226840800	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr1:226823200-226841400	Weak transcription	NHDF-Ad	bronchial
4	chr1:226829400-226843800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:226830400-226840400	Genic enhancers	Primary T cells from cord blood	blood
6	chr1:226830400-226840400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:226831400-226841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:226832000-226843800	Weak transcription	HMEC	breast
9	chr1:226832400-226843600	Weak transcription	Stomach Mucosa	stomach
10	chr1:226833000-226838800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:226833600-226844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:226833800-226841600	Weak transcription	Fetal Heart	heart
13	chr1:226834400-226838600	Weak transcription	Psoas Muscle	Psoas
14	chr1:226834600-226841400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:226835200-226841600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:226835800-226841000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:226836000-226840800	Weak transcription	Colonic Mucosa	Colon
18	chr1:226836000-226841200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:226836000-226841400	Weak transcription	NHLF	lung
20	chr1:226836000-226844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:226836000-226844200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:226836200-226842000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:226836200-226842000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:226836400-226841200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:226836400-226847200	Weak transcription	Ovary	ovary
26	chr1:226836600-226841400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:226836600-226841400	Weak transcription	Fetal Intestine Large	intestine
28	chr1:226836600-226841400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:226836800-226839600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:226836800-226856200	Enhancers	Left Ventricle	heart
31	chr1:226837000-226838800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:226837000-226841400	Weak transcription	Fetal Intestine Small	intestine
33	chr1:226837000-226842200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:226837000-226843800	Enhancers	Colon Smooth Muscle	Colon
35	chr1:226837000-226849800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr1:226837200-226838800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:226837200-226839000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:226837200-226839600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:226837200-226840000	Weak transcription	GM12878-XiMat	blood
40	chr1:226837200-226840800	Enhancers	Brain Angular Gyrus	brain
41	chr1:226837200-226841000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:226837200-226841000	Weak transcription	Fetal Lung	lung
43	chr1:226837200-226842200	Weak transcription	Liver	Liver
44	chr1:226837200-226843000	Enhancers	Brain Hippocampus Middle	brain
45	chr1:226837200-226844800	Enhancers	Right Ventricle	heart
46	chr1:226837200-226846000	Enhancers	Brain Anterior Caudate	brain
47	chr1:226837400-226838600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:226837400-226838800	Weak transcription	Pancreas	Pancrea
49	chr1:226837400-226839600	Weak transcription	Primary B cells from cord blood	blood
50	chr1:226837400-226840400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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