Variant report

Variant	rs16929780
Chromosome Location	chr12:26123834-26123835
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	chr12:26110508..26112354-chr12:26121125..26124045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123094	Chromatin interaction
ENSG00000246695	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10505989	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs10842654	0.87[CEU][hapmap]
rs12425863	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426668	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs1495649	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533244	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929681	0.84[CHB][hapmap]
rs16929815	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929857	0.84[AMR][1000 genomes]
rs16929860	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929894	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929895	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929904	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929970	0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs16929998	0.87[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs2137550	0.92[JPT][hapmap]
rs2343200	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2669565	0.92[JPT][hapmap]
rs2669566	0.92[JPT][hapmap]
rs2669568	0.83[JPT][hapmap]
rs2729626	0.92[JPT][hapmap]
rs2729638	0.82[JPT][hapmap]
rs2729643	0.83[JPT][hapmap]
rs2729644	0.84[JPT][hapmap]
rs2729649	0.84[JPT][hapmap]
rs3803008	0.84[AMR][1000 genomes]
rs4963643	0.91[AMR][1000 genomes]
rs4963644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963952	0.92[JPT][hapmap]
rs57082706	0.81[AMR][1000 genomes]
rs57791860	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61123975	0.81[AMR][1000 genomes]
rs6487526	0.83[JPT][hapmap]
rs73074872	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73074898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077161	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73077176	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73077179	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73079010	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73079023	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73079024	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73079069	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73080925	0.81[AMR][1000 genomes]
rs7961722	0.92[JPT][hapmap]
rs9804876	0.87[CEU][hapmap];0.83[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	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26113400-26126200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:26113400-26128800	Weak transcription	HSMM	muscle
3	chr12:26113800-26124000	Weak transcription	Fetal Intestine Large	intestine
4	chr12:26114000-26126600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:26114000-26128000	Weak transcription	Fetal Intestine Small	intestine
6	chr12:26114200-26125600	Weak transcription	HMEC	breast
7	chr12:26115000-26127800	Weak transcription	Fetal Kidney	kidney
8	chr12:26116600-26124600	Weak transcription	NHLF	lung
9	chr12:26117000-26126200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:26117200-26124000	Weak transcription	Fetal Stomach	stomach
11	chr12:26117200-26130200	Weak transcription	Fetal Heart	heart
12	chr12:26117400-26126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
14	chr12:26118400-26131600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:26119600-26124400	Enhancers	Brain Hippocampus Middle	brain
16	chr12:26119600-26130200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:26119800-26124400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:26120000-26124000	Enhancers	Colon Smooth Muscle	Colon
19	chr12:26120000-26125000	Enhancers	Brain Anterior Caudate	brain
20	chr12:26120000-26127400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:26120200-26124600	Enhancers	Brain Substantia Nigra	brain
22	chr12:26120600-26125000	Enhancers	Ovary	ovary
23	chr12:26120600-26125000	Enhancers	Psoas Muscle	Psoas
24	chr12:26121000-26131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:26121200-26124000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:26121200-26126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:26121200-26129600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:26121600-26124800	Enhancers	HUVEC	blood vessel
29	chr12:26121800-26124400	Enhancers	Lung	lung
30	chr12:26121800-26125000	Enhancers	Right Atrium	heart
31	chr12:26122000-26125000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:26122200-26125000	Enhancers	NH-A	brain
33	chr12:26122200-26126200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:26122400-26124000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:26122400-26124400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:26122400-26124400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr12:26122400-26126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:26122400-26128200	Enhancers	Osteobl	bone
39	chr12:26122600-26124200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:26122600-26126800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:26122600-26127200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:26122800-26125200	Enhancers	Aorta	Aorta
43	chr12:26123000-26124000	Enhancers	Stomach Smooth Muscle	stomach
44	chr12:26123000-26124800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr12:26123200-26124600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr12:26123200-26127000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:26123400-26124200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:26123400-26124400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:26123400-26125000	Enhancers	Adipose Nuclei	Adipose
50	chr12:26123400-26125000	Enhancers	Fetal Muscle Leg	muscle

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