Variant report

Variant	rs12220354
Chromosome Location	chr10:27127282-27127283
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	chr10:27125897..27127409-chr10:27129150..27132076,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10829066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11015244	0.82[YRI][hapmap]
rs11015256	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11015257	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11015264	0.87[EUR][1000 genomes]
rs11015277	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015278	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11015282	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11015287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015290	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11015297	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015303	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11015315	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11015316	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11813623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11814449	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12220461	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12221372	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17816509	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17816641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1998633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2148111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2505971	1.00[JPT][hapmap]
rs3802615	0.87[ASN][1000 genomes]
rs3802616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4749188	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4749190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4749193	0.86[EUR][1000 genomes]
rs4749194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7910986	0.82[AMR][1000 genomes];0.86[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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv11591	chr10:27117697-27135748	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27095000-27130600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr10:27095000-27138600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:27095400-27129800	Weak transcription	NHEK	skin
4	chr10:27095600-27129000	Weak transcription	Right Atrium	heart
5	chr10:27095600-27132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:27095600-27148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:27099800-27128800	Weak transcription	K562	blood
8	chr10:27101800-27129000	Weak transcription	Stomach Mucosa	stomach
9	chr10:27104800-27129200	Weak transcription	Colonic Mucosa	Colon
10	chr10:27107000-27129000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:27107400-27129000	Weak transcription	Spleen	Spleen
12	chr10:27109400-27132600	Weak transcription	HMEC	breast
13	chr10:27110000-27130400	Weak transcription	HUVEC	blood vessel
14	chr10:27111800-27129000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:27111800-27129200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:27111800-27147000	Weak transcription	Fetal Intestine Large	intestine
17	chr10:27112000-27128800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:27112000-27130400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:27112400-27129000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:27112800-27129000	Weak transcription	Primary B cells from cord blood	blood
21	chr10:27112800-27129000	Weak transcription	Brain Anterior Caudate	brain
22	chr10:27112800-27129000	Weak transcription	Small Intestine	intestine
23	chr10:27119400-27129000	Weak transcription	Aorta	Aorta
24	chr10:27119600-27130400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:27119600-27133600	Weak transcription	Thymus	Thymus
26	chr10:27119600-27147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:27120000-27128800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:27120000-27129200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr10:27120600-27142600	Weak transcription	HepG2	liver
30	chr10:27120800-27127400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr10:27121000-27129800	Weak transcription	Fetal Brain Female	brain
32	chr10:27121200-27130800	Weak transcription	Dnd41	blood
33	chr10:27122200-27128800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:27122200-27128800	Weak transcription	Lung	lung
35	chr10:27122200-27129200	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:27122400-27129200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:27122600-27129000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:27122600-27129200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:27122600-27133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr10:27122600-27136800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:27122600-27143400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr10:27123000-27128800	Weak transcription	Left Ventricle	heart
43	chr10:27123000-27145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr10:27123800-27129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr10:27124400-27146200	Weak transcription	Fetal Muscle Leg	muscle
46	chr10:27124800-27129000	Weak transcription	Fetal Thymus	thymus
47	chr10:27125000-27130400	Weak transcription	Fetal Stomach	stomach
48	chr10:27125000-27131600	Weak transcription	Fetal Intestine Small	intestine
49	chr10:27125400-27128000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr10:27125600-27128600	Weak transcription	Primary T cells from cord blood	blood

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