Variant report

Variant	rs28570232
Chromosome Location	chr2:48560052-48560053
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48559983..48562796-chr2:48566723..48568963,3	K562	blood:
2	chr2:48558442..48561276-chr2:48561458..48563692,2	K562	blood:
3	chr2:48517525..48519074-chr2:48557962..48560768,2	K562	blood:
4	chr2:48559522..48562446-chr2:48563870..48566960,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251889	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17037271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28399967	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28439229	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485447	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595126	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34136171	0.85[EUR][1000 genomes]
rs56879885	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57729372	0.86[AFR][1000 genomes]
rs60743061	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62137000	0.82[AFR][1000 genomes]
rs6545031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737455	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72887650	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72887686	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7576648	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9677579	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[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	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
4	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
5	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543400-48568600	Weak transcription	HSMM	muscle
2	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:48544400-48570400	Weak transcription	NHEK	skin
5	chr2:48544400-48570800	Weak transcription	HMEC	breast
6	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
9	chr2:48552400-48561000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:48552400-48561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:48552400-48566200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
13	chr2:48553400-48574400	Weak transcription	Lung	lung
14	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
15	chr2:48554400-48561000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:48554800-48561600	Weak transcription	Psoas Muscle	Psoas
18	chr2:48554800-48562000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:48555000-48560400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:48555000-48560400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:48555000-48561600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:48555000-48562000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:48555200-48560800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:48555400-48570600	Weak transcription	NHLF	lung
25	chr2:48556000-48560400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:48556800-48560400	Enhancers	Primary B cells from cord blood	blood
27	chr2:48556800-48562800	Enhancers	Brain Angular Gyrus	brain
28	chr2:48556800-48570600	Weak transcription	Fetal Thymus	thymus
29	chr2:48556800-48571600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:48557000-48560200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:48557000-48566600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:48557000-48567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:48557200-48564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:48557200-48568600	Weak transcription	HUVEC	blood vessel
37	chr2:48557800-48560800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:48557800-48560800	Enhancers	Primary T cells from cord blood	blood
39	chr2:48557800-48561400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:48557800-48570400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:48558000-48561200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:48558200-48560600	Weak transcription	HepG2	liver
43	chr2:48558200-48560800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:48558200-48560800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:48558200-48568200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:48558400-48571400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:48558800-48560400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:48558800-48561200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:48558800-48561400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:48558800-48566600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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