Variant report

Variant	rs17037271
Chromosome Location	chr2:48552129-48552130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48551728..48554180-chr2:48555389..48557801,2	MCF-7	breast:
2	chr2:48541080..48542668-chr2:48550192..48552132,2	MCF-7	breast:
3	chr2:48550181..48552303-chr2:48565867..48568039,2	K562	blood:
4	chr2:48552083..48554152-chr2:48555088..48558115,3	K562	blood:
5	chr2:48541852..48543622-chr2:48550647..48553258,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251889	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs28399967	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28439229	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28485447	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28570232	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28595126	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34136171	0.83[EUR][1000 genomes]
rs56879885	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60743061	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6545031	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6545033	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6737455	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72887650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72887686	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7576648	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9677579	0.90[AMR][1000 genomes];0.85[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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543200-48553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:48543400-48553000	Weak transcription	Lung	lung
3	chr2:48543400-48553000	Weak transcription	Psoas Muscle	Psoas
4	chr2:48543400-48568600	Weak transcription	HSMM	muscle
5	chr2:48543600-48552200	Weak transcription	Osteobl	bone
6	chr2:48543600-48553200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:48543600-48553400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:48543600-48554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:48543600-48555400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:48543600-48556600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
15	chr2:48544400-48556200	Weak transcription	NHDF-Ad	bronchial
16	chr2:48544400-48558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:48544400-48570400	Weak transcription	NHEK	skin
18	chr2:48544400-48570800	Weak transcription	HMEC	breast
19	chr2:48544600-48558600	Weak transcription	Spleen	Spleen
20	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:48544800-48559400	Weak transcription	Right Atrium	heart
22	chr2:48546600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:48547400-48554600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:48548200-48552200	Weak transcription	Liver	Liver
25	chr2:48548200-48555200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:48548400-48552400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:48548400-48553000	Weak transcription	Small Intestine	intestine
28	chr2:48548400-48553200	Weak transcription	Adipose Nuclei	Adipose
29	chr2:48548400-48555200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:48548400-48556600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:48549800-48555000	Weak transcription	Dnd41	blood
33	chr2:48550000-48553200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:48550000-48553400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:48550000-48553800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:48550400-48554600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr2:48550400-48554600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:48550400-48554600	Enhancers	HepG2	liver
39	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
40	chr2:48550600-48552600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:48550600-48559400	Enhancers	Brain Hippocampus Middle	brain
42	chr2:48550800-48552800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:48550800-48554200	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:48551000-48552200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:48551000-48553000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr2:48551200-48553400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:48551400-48552400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:48551400-48552400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr2:48551400-48552400	Enhancers	K562	blood
50	chr2:48551400-48554000	Enhancers	Primary neutrophils fromperipheralblood	blood

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