Variant report

Variant	rs12563400
Chromosome Location	chr1:93064823-93064824
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	chr1:92775257..92776314-chr1:93064696..93065442,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1003209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10127800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10159031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465755	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075243	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12564335	1.00[ASN][1000 genomes]
rs12564537	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12564911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12565259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12566527	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12568629	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17131636	1.00[CEU][hapmap]
rs17131655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2151575	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391198	1.00[JPT][hapmap]
rs3762277	1.00[CHB][hapmap]
rs56144352	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56172716	0.89[EUR][1000 genomes]
rs57782462	0.89[EUR][1000 genomes]
rs59459727	0.89[EUR][1000 genomes]
rs60855457	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61288876	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61457032	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699723	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs74101167	0.84[ASN][1000 genomes]
rs74101184	0.89[EUR][1000 genomes]
rs74101186	0.89[EUR][1000 genomes]
rs74101190	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74101199	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74102906	0.89[EUR][1000 genomes]
rs74102921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74102923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74102948	0.89[EUR][1000 genomes]
rs74102953	0.89[EUR][1000 genomes]
rs7535171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969698	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]

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	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1004381	chr1:92968173-93064823	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830603	chr1:93003657-93172206	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92983600-93066200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:92994600-93066000	Weak transcription	Placenta	Placenta
3	chr1:93004400-93070000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:93014800-93100200	Weak transcription	Right Ventricle	heart
5	chr1:93017000-93066000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:93026000-93091800	Weak transcription	Hela-S3	cervix
7	chr1:93027400-93066000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:93030000-93082200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:93034400-93081000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:93043200-93070000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:93045800-93070000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:93046800-93070200	Weak transcription	Brain Anterior Caudate	brain
13	chr1:93050200-93081200	Weak transcription	HSMMtube	muscle
14	chr1:93050600-93069400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:93050600-93082400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:93050600-93082600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:93051600-93067200	Weak transcription	HUVEC	blood vessel
18	chr1:93051800-93082000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:93052000-93066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:93052000-93069800	Weak transcription	Liver	Liver
21	chr1:93052000-93070000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:93052000-93119400	Weak transcription	NHEK	skin
23	chr1:93053200-93070000	Weak transcription	Colonic Mucosa	Colon
24	chr1:93053400-93066600	Weak transcription	Primary T cells from cord blood	blood
25	chr1:93053600-93166200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:93054800-93065200	Weak transcription	Primary B cells from cord blood	blood
27	chr1:93054800-93089200	Weak transcription	HSMM	muscle
28	chr1:93055000-93080800	Weak transcription	Aorta	Aorta
29	chr1:93055000-93082600	Weak transcription	Pancreas	Pancrea
30	chr1:93055000-93083000	Weak transcription	Fetal Lung	lung
31	chr1:93055000-93100200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:93055200-93069800	Weak transcription	Ovary	ovary
33	chr1:93055200-93082600	Weak transcription	Lung	lung
34	chr1:93055400-93069400	Weak transcription	Fetal Intestine Large	intestine
35	chr1:93055400-93069400	Weak transcription	Fetal Stomach	stomach
36	chr1:93055400-93069400	Weak transcription	Left Ventricle	heart
37	chr1:93055800-93069600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:93055800-93081000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:93055800-93082200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:93055800-93082200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:93055800-93085200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:93056200-93069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:93059000-93066000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:93060000-93066200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:93061800-93081200	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:93062000-93066000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:93062000-93069400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:93062000-93118800	Weak transcription	HMEC	breast
49	chr1:93063000-93100600	Weak transcription	Gastric	stomach
50	chr1:93063800-93069200	Weak transcription	Fetal Intestine Small	intestine

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