Variant report

Variant	rs28387040
Chromosome Location	chr12:121959790-121959791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121958031..121962041-chr12:121975290..121977508,3	MCF-7	breast:
2	chr12:121958437..121960268-chr12:121962463..121965100,2	MCF-7	breast:
3	chr12:121957217..121960206-chr12:122075609..122077244,2	K562	blood:
4	chr12:121959310..121962414-chr12:121967014..121969071,3	MCF-7	breast:
5	chr12:121955418..121960575-chr12:121960736..121964732,5	K562	blood:
6	chr12:121956591..121958416-chr12:121958479..121960650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11065608	1.00[AMR][1000 genomes]
rs28508242	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538950	0.87[EUR][1000 genomes]
rs28617424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28620034	0.95[ASN][1000 genomes]
rs28637695	0.98[ASN][1000 genomes]
rs61667355	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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	nsv560457	chr12:121956483-121976176	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121928600-121965800	Weak transcription	Hela-S3	cervix
2	chr12:121932000-121974400	Weak transcription	NHEK	skin
3	chr12:121934800-121968200	Weak transcription	Small Intestine	intestine
4	chr12:121938200-121968600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:121938200-121971000	Weak transcription	Stomach Mucosa	stomach
6	chr12:121938200-121973800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:121938400-121968600	Weak transcription	Fetal Kidney	kidney
8	chr12:121938400-121973600	Weak transcription	Psoas Muscle	Psoas
9	chr12:121938600-121959800	Weak transcription	NH-A	brain
10	chr12:121938800-121968600	Weak transcription	Right Atrium	heart
11	chr12:121938800-121970600	Weak transcription	Fetal Brain Male	brain
12	chr12:121939200-121961600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:121939800-121961000	Weak transcription	Colonic Mucosa	Colon
14	chr12:121943800-121968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:121944000-121968400	Weak transcription	Osteobl	bone
16	chr12:121947600-121968200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:121947800-121968800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:121947800-121969400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:121947800-121973400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:121948000-121960600	Weak transcription	Brain Substantia Nigra	brain
21	chr12:121948000-121968400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:121948200-121973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:121950200-121973800	Weak transcription	HSMMtube	muscle
24	chr12:121952400-121960600	Weak transcription	Brain Anterior Caudate	brain
25	chr12:121952400-121968400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:121952600-121968200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:121952600-121968600	Weak transcription	A549	lung
28	chr12:121953400-121961200	Strong transcription	Fetal Stomach	stomach
29	chr12:121953400-121970600	Strong transcription	Fetal Intestine Small	intestine
30	chr12:121953600-121963000	Strong transcription	Primary T cells from cord blood	blood
31	chr12:121953800-121959800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr12:121954000-121967800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:121954200-121964400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:121954200-121964800	Strong transcription	Thymus	Thymus
35	chr12:121954600-121964800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:121956000-121961000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:121956000-121964600	Strong transcription	Dnd41	blood
38	chr12:121956200-121959800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:121956200-121962200	Strong transcription	Fetal Intestine Large	intestine
40	chr12:121956200-121963600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:121956200-121964400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:121956200-121964400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:121956400-121959800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:121956400-121963800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:121956400-121964400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:121956600-121959800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:121956600-121959800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:121956600-121959800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:121956600-121961000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:121957000-121960000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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