Variant report

Variant	rs12123837
Chromosome Location	chr1:172153897-172153898
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	chr1:172146908..172150355-chr1:172151675..172155662,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10489297	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911270	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484597	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584955	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589142	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126381	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129264	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129806	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135520	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277127	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361886	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361920	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361955	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2209096	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209098	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224782	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421990	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421991	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915514	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394690	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55935473	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138708	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593688	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807788	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628479	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535241	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979021	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172147400-172154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:172150000-172154000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:172150000-172154200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172150200-172154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:172150800-172154000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:172150800-172155600	Enhancers	Fetal Lung	lung
7	chr1:172150800-172159000	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:172151000-172154000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:172151000-172154400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:172151000-172160800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:172151200-172154200	Weak transcription	Fetal Intestine Large	intestine
12	chr1:172151600-172154000	Weak transcription	A549	lung
13	chr1:172151600-172154200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:172151600-172154200	Weak transcription	Hela-S3	cervix
15	chr1:172151600-172154800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:172151800-172154200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:172151800-172154200	Weak transcription	Stomach Mucosa	stomach
18	chr1:172151800-172154200	Enhancers	GM12878-XiMat	blood
19	chr1:172152000-172154000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:172152000-172154000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:172152000-172154200	Weak transcription	Fetal Heart	heart
22	chr1:172152000-172154400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:172152200-172154000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:172152200-172154400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:172152200-172154600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:172152400-172154000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:172152400-172154000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:172152400-172154200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:172152400-172154200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:172152400-172154200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:172152400-172154200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:172152400-172154600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:172152800-172155600	Enhancers	Ovary	ovary
34	chr1:172152800-172156000	Enhancers	Fetal Muscle Leg	muscle
35	chr1:172153200-172157800	Enhancers	Primary B cells from cord blood	blood
36	chr1:172153400-172154200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:172153400-172154600	Enhancers	NHEK	skin
38	chr1:172153400-172154800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:172153400-172154800	Enhancers	Fetal Intestine Small	intestine
40	chr1:172153400-172155800	Enhancers	Fetal Stomach	stomach
41	chr1:172153600-172154000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:172153600-172154400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:172153600-172154600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:172153600-172154600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:172153600-172154800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:172153600-172154800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:172153600-172154800	Enhancers	Small Intestine	intestine
48	chr1:172153600-172155400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:172153600-172155400	Enhancers	Osteobl	bone
50	chr1:172153600-172155600	Enhancers	NHDF-Ad	bronchial

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