Variant report

Variant	rs11895933
Chromosome Location	chr2:54767792-54767793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPYL6-2	chr2:54767736-54767834	ENSG00000228108.1

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10166179	1.00[EUR][1000 genomes]
rs10188600	1.00[EUR][1000 genomes]
rs1030601	1.00[EUR][1000 genomes]
rs11885098	1.00[EUR][1000 genomes]
rs13386997	1.00[EUR][1000 genomes]
rs13394958	1.00[EUR][1000 genomes]
rs13409783	1.00[EUR][1000 genomes]
rs13419870	1.00[EUR][1000 genomes]
rs3936082	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4671950	0.82[LWK][hapmap]
rs56726104	1.00[EUR][1000 genomes]
rs61332964	1.00[EUR][1000 genomes]
rs61743072	1.00[EUR][1000 genomes]
rs6545436	1.00[EUR][1000 genomes]
rs6545439	1.00[EUR][1000 genomes]
rs6729826	0.87[ASW][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs6753590	1.00[EUR][1000 genomes]
rs6753689	1.00[EUR][1000 genomes]
rs6756814	1.00[EUR][1000 genomes]
rs6757017	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72918768	1.00[EUR][1000 genomes]
rs73932784	1.00[EUR][1000 genomes]
rs73934323	1.00[EUR][1000 genomes]
rs7559157	0.93[AMR][1000 genomes];1.00[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
7	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
10	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
16	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
18	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:54760800-54767800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:54761200-54768800	Strong transcription	HSMM	muscle
22	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
23	chr2:54761800-54769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:54762200-54770400	Weak transcription	Fetal Kidney	kidney
26	chr2:54762200-54772800	Weak transcription	Aorta	Aorta
27	chr2:54762200-54772800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:54762400-54770800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:54762400-54772600	Weak transcription	Liver	Liver
31	chr2:54762800-54772600	Weak transcription	NHDF-Ad	bronchial
32	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:54763200-54770800	Weak transcription	Fetal Intestine Small	intestine
34	chr2:54763200-54772600	Weak transcription	NHLF	lung
35	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:54764400-54767800	Strong transcription	Adipose Nuclei	Adipose
37	chr2:54764400-54768000	Weak transcription	Ovary	ovary
38	chr2:54764400-54768800	Strong transcription	HSMMtube	muscle
39	chr2:54764400-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:54764600-54769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:54764600-54772600	Weak transcription	Osteobl	bone
42	chr2:54764800-54769400	Weak transcription	Fetal Stomach	stomach
43	chr2:54764800-54769400	Weak transcription	Psoas Muscle	Psoas
44	chr2:54765000-54768200	Enhancers	A549	lung
45	chr2:54765600-54768600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
47	chr2:54766000-54768400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:54766000-54769600	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:54766200-54767800	Strong transcription	Fetal Lung	lung
50	chr2:54766200-54768400	Enhancers	Skeletal Muscle Male	skeletal muscle

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