Variant report

Variant	rs2417848
Chromosome Location	chr12:20364562-20364563
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	chr12:20357490..20359310-chr12:20364032..20366032,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10431212	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10444397	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10770624	0.80[EUR][1000 genomes]
rs10770627	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2195280	0.85[AMR][1000 genomes]
rs4545637	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7307541	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035141	chr12:20286595-20429040	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv557700	chr12:20346383-20379710	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv898857	chr12:20359670-20423727	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20356000-20364600	Weak transcription	Aorta	Aorta
2	chr12:20356400-20365400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr12:20356600-20364600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:20359600-20364600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:20362200-20367200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:20362600-20364600	Weak transcription	Adipose Nuclei	Adipose
7	chr12:20362600-20365400	Weak transcription	Right Atrium	heart
8	chr12:20362600-20365600	Weak transcription	Left Ventricle	heart
9	chr12:20362800-20364600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:20362800-20364800	Weak transcription	Right Ventricle	heart
11	chr12:20362800-20365000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:20363200-20365200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:20363200-20365600	Enhancers	Primary B cells from cord blood	blood
14	chr12:20363200-20366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:20363400-20365800	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:20363400-20365800	Enhancers	Hela-S3	cervix
17	chr12:20363600-20364600	Weak transcription	Ovary	ovary
18	chr12:20363800-20364800	Enhancers	Duodenum Mucosa	Duodenum
19	chr12:20363800-20365400	Enhancers	NH-A	brain
20	chr12:20363800-20366000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:20364000-20366200	Enhancers	Fetal Muscle Leg	muscle
22	chr12:20364000-20366200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr12:20364000-20367800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:20364000-20368000	Enhancers	Fetal Stomach	stomach
25	chr12:20364200-20364800	Enhancers	Brain Substantia Nigra	brain
26	chr12:20364200-20365000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr12:20364200-20365000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr12:20364200-20366400	Enhancers	Fetal Intestine Large	intestine
29	chr12:20364200-20366400	Enhancers	Fetal Intestine Small	intestine
30	chr12:20364200-20366600	Enhancers	Small Intestine	intestine
31	chr12:20364200-20367600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:20364400-20364600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:20364400-20365200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr12:20364400-20365400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:20364400-20365800	Enhancers	Fetal Brain Male	brain
36	chr12:20364400-20366000	Enhancers	Colon Smooth Muscle	Colon
37	chr12:20364400-20366200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr12:20364400-20366400	Flanking Active TSS	A549	lung
39	chr12:20364400-20366800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:20364400-20367000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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