Variant report

Variant	rs55903525
Chromosome Location	chr2:54749228-54749229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54749225..54752072-chr2:54796311..54798001,2	K562	blood:
2	chr2:54749018..54751873-chr2:54799647..54801248,2	MCF-7	breast:
3	chr2:54748253..54750106-chr2:54930790..54932794,2	MCF-7	breast:
4	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:
5	chr2:54747821..54752887-chr2:54784386..54788690,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs41426349	0.81[EUR][1000 genomes]
rs62134669	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62134670	0.89[EUR][1000 genomes]
rs62134673	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545412	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6724374	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
4	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
5	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
8	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
9	chr2:54740600-54749800	Weak transcription	HepG2	liver
10	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:54742800-54750600	Weak transcription	Brain Germinal Matrix	brain
13	chr2:54743600-54751600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:54744400-54751400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:54744400-54753400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:54744400-54753400	Weak transcription	Ovary	ovary
18	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
19	chr2:54744600-54753400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:54746200-54749400	Enhancers	NHDF-Ad	bronchial
21	chr2:54746200-54750200	Weak transcription	Fetal Kidney	kidney
22	chr2:54746400-54749800	Weak transcription	Liver	Liver
23	chr2:54746600-54749600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54746600-54751600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:54746800-54749800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:54746800-54750400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:54747200-54750200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:54747200-54750600	Weak transcription	Gastric	stomach
31	chr2:54747200-54750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:54747200-54750800	Weak transcription	Psoas Muscle	Psoas
33	chr2:54747200-54751400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:54747200-54751600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:54747200-54751600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:54747200-54753200	Weak transcription	Fetal Brain Female	brain
37	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:54747400-54749800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:54747400-54750400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:54747400-54750600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:54747400-54751400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:54747400-54751600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:54747400-54753600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:54747600-54751400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:54747800-54752400	Enhancers	Brain Hippocampus Middle	brain
47	chr2:54747800-54753400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:54748000-54749600	Enhancers	Lung	lung
49	chr2:54748200-54750400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:54748200-54750600	Weak transcription	Rectal Smooth Muscle	rectum

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