Variant report

Variant	rs11885098
Chromosome Location	chr2:54758602-54758603
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
2	chr2:54196354..54198285-chr2:54758115..54760291,3	MCF-7	breast:
3	chr2:54757446..54759466-chr2:54767763..54770756,2	K562	blood:
4	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000228108	Chromatin interaction

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

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

rs_ID	r²[population]
rs10166179	1.00[EUR][1000 genomes]
rs10188600	1.00[EUR][1000 genomes]
rs1030601	1.00[EUR][1000 genomes]
rs11895933	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	1.00[EUR][1000 genomes]
rs56726104	1.00[EUR][1000 genomes]
rs61332964	1.00[EUR][1000 genomes]
rs61743072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545436	1.00[EUR][1000 genomes]
rs6545439	1.00[EUR][1000 genomes]
rs6753590	1.00[EUR][1000 genomes]
rs6753689	1.00[EUR][1000 genomes]
rs6756814	1.00[EUR][1000 genomes]
rs6757017	1.00[EUR][1000 genomes]
rs72918768	1.00[EUR][1000 genomes]
rs73932784	1.00[EUR][1000 genomes]
rs73934323	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73934326	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7559157	1.00[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	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
10	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
16	chr2:54752000-54764600	Weak transcription	Gastric	stomach
17	chr2:54752200-54759600	Weak transcription	Small Intestine	intestine
18	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:54752400-54759600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
22	chr2:54753000-54758800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:54753000-54759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
25	chr2:54753400-54758800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:54754000-54760200	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:54754400-54759800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:54754600-54760000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:54754800-54759000	Strong transcription	HSMM	muscle
33	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:54755000-54758800	Weak transcription	Lung	lung
35	chr2:54755000-54761000	Weak transcription	Right Ventricle	heart
36	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:54755200-54759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:54755400-54762600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr2:54755600-54761200	Weak transcription	Fetal Brain Male	brain
40	chr2:54756000-54759400	Strong transcription	Fetal Stomach	stomach
41	chr2:54756200-54758800	Genic enhancers	HepG2	liver
42	chr2:54756400-54759000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54756400-54759200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:54756400-54759800	Strong transcription	HSMMtube	muscle
45	chr2:54756600-54759000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
47	chr2:54756800-54758800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:54756800-54759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
50	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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