Variant report

Variant	rs12417273
Chromosome Location	chr11:120307596-120307597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120205769..120208609-chr11:120306177..120309218,3	MCF-7	breast:
2	chr11:120265069..120267317-chr11:120306799..120308783,2	K562	blood:
3	chr11:120302832..120305413-chr11:120306249..120308301,2	K562	blood:

Variant related genes	Relation type
ENSG00000196914	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10502236	0.97[ASN][1000 genomes]
rs10892579	0.91[ASN][1000 genomes]
rs12417436	1.00[EUR][1000 genomes]
rs12418151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12418325	0.91[ASN][1000 genomes]
rs12418329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12418336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12419091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12419759	1.00[AMR][1000 genomes]
rs12420409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12420968	1.00[AMR][1000 genomes]
rs12421291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12421331	1.00[AMR][1000 genomes]
rs12421477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2305009	1.00[EUR][1000 genomes]
rs3740739	1.00[EUR][1000 genomes]
rs3740740	1.00[EUR][1000 genomes]
rs3758693	1.00[EUR][1000 genomes]
rs4054	1.00[AMR][1000 genomes]
rs57912596	0.97[ASN][1000 genomes]
rs7108596	0.97[ASN][1000 genomes]
rs7110955	0.88[ASN][1000 genomes]
rs7948299	0.91[ASN][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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1051672	chr11:120238962-120314178	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1051783	chr11:120246224-120314178	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120272200-120315600	Weak transcription	Brain Germinal Matrix	brain
2	chr11:120272200-120315800	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:120272400-120320600	Weak transcription	Psoas Muscle	Psoas
4	chr11:120275600-120322200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:120275800-120314000	Weak transcription	Right Ventricle	heart
6	chr11:120277600-120319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:120285600-120319800	Weak transcription	Gastric	stomach
8	chr11:120288600-120309600	Weak transcription	Aorta	Aorta
9	chr11:120290000-120308200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:120290400-120313400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:120291800-120319200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:120292000-120315400	Weak transcription	Colonic Mucosa	Colon
13	chr11:120293000-120309000	Weak transcription	Fetal Stomach	stomach
14	chr11:120294000-120316000	Weak transcription	Primary B cells from cord blood	blood
15	chr11:120295400-120312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:120295400-120318600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:120296000-120308400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:120296000-120309200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:120296000-120312400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:120296000-120315800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:120296000-120316200	Weak transcription	Esophagus	oesophagus
22	chr11:120296000-120316400	Weak transcription	Lung	lung
23	chr11:120296000-120317600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:120296200-120308400	Weak transcription	Adipose Nuclei	Adipose
25	chr11:120296200-120315400	Weak transcription	Fetal Brain Male	brain
26	chr11:120296400-120308400	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:120296400-120308400	Weak transcription	HepG2	liver
28	chr11:120299600-120308200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:120300600-120308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:120300600-120312000	Strong transcription	Liver	Liver
31	chr11:120300800-120308400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:120301400-120308000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:120301400-120355200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr11:120302600-120308000	Weak transcription	Fetal Intestine Large	intestine
35	chr11:120302600-120308200	Weak transcription	Brain Angular Gyrus	brain
36	chr11:120302600-120310000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:120302600-120312400	Weak transcription	Left Ventricle	heart
38	chr11:120302600-120316200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:120302800-120317400	Weak transcription	Small Intestine	intestine
40	chr11:120303000-120312600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr11:120303000-120313400	Weak transcription	Ovary	ovary
42	chr11:120303000-120317000	Weak transcription	K562	blood
43	chr11:120303000-120317400	Weak transcription	Pancreas	Pancrea
44	chr11:120303000-120319400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:120303200-120308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:120303200-120312400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:120303200-120312600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:120303200-120312600	Weak transcription	Brain Substantia Nigra	brain
49	chr11:120303200-120312600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:120303200-120312800	Weak transcription	Stomach Smooth Muscle	stomach

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