Variant report

Variant	rs829578
Chromosome Location	chr2:30680232-30680233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30668373..30671369-chr2:30677900..30680714,3	MCF-7	breast:
2	chr2:30677517..30682510-chr2:30682594..30687236,9	K562	blood:
3	chr2:30678439..30680245-chr2:30728764..30731252,2	K562	blood:
4	chr2:30678530..30680872-chr2:30685623..30687236,2	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1252624	0.89[EUR][1000 genomes]
rs1252625	0.89[EUR][1000 genomes]
rs1252646	0.89[EUR][1000 genomes]
rs2167969	0.87[EUR][1000 genomes]
rs2692035	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952147	0.87[EUR][1000 genomes]
rs6749074	0.86[EUR][1000 genomes]
rs829574	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829582	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829583	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829618	0.89[EUR][1000 genomes]
rs829619	0.83[EUR][1000 genomes]
rs829620	0.85[EUR][1000 genomes]
rs829622	0.89[EUR][1000 genomes]
rs829631	0.83[EUR][1000 genomes]
rs829634	0.89[EUR][1000 genomes]
rs829641	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829642	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829646	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829654	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829655	0.85[EUR][1000 genomes]
rs829659	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829661	0.85[EUR][1000 genomes]
rs829662	0.85[EUR][1000 genomes]
rs829663	0.85[EUR][1000 genomes]
rs829669	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829670	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829671	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829672	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829673	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829675	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829677	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829679	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829680	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs844194	0.89[EUR][1000 genomes]
rs9309680	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671000-30682000	Weak transcription	Aorta	Aorta
2	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:30671200-30681200	Weak transcription	Right Atrium	heart
4	chr2:30671200-30688200	Weak transcription	HSMM	muscle
5	chr2:30671600-30682000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:30671600-30682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:30671600-30683800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:30671600-30685600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:30671800-30681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:30672000-30680600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:30672000-30681000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:30672000-30681200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:30672000-30681800	Weak transcription	Primary B cells from cord blood	blood
19	chr2:30672000-30682000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:30672000-30684600	Weak transcription	Hela-S3	cervix
21	chr2:30672000-30686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:30672000-30686800	Weak transcription	Dnd41	blood
23	chr2:30672000-30688000	Weak transcription	Fetal Lung	lung
24	chr2:30672800-30682600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:30673600-30681400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:30673800-30681400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:30674200-30687400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:30675800-30681600	Weak transcription	Primary T cells from cord blood	blood
29	chr2:30675800-30682000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:30675800-30682200	Enhancers	HepG2	liver
31	chr2:30676200-30681200	Weak transcription	Psoas Muscle	Psoas
32	chr2:30677400-30680400	Enhancers	Fetal Intestine Small	intestine
33	chr2:30677400-30681800	Enhancers	Fetal Intestine Large	intestine
34	chr2:30677800-30683800	Enhancers	Fetal Heart	heart
35	chr2:30678000-30680400	Enhancers	K562	blood
36	chr2:30678200-30684200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr2:30678200-30684200	Weak transcription	A549	lung
38	chr2:30678400-30682000	Weak transcription	Right Ventricle	heart
39	chr2:30678400-30682400	Weak transcription	Gastric	stomach
40	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
41	chr2:30678600-30681800	Weak transcription	Stomach Mucosa	stomach
42	chr2:30678600-30688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:30678600-30710600	Weak transcription	NHLF	lung
45	chr2:30678800-30681000	Weak transcription	Small Intestine	intestine
46	chr2:30678800-30687800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:30679000-30682600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:30679000-30683600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:30679000-30684200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:30679200-30680400	Enhancers	Thymus	Thymus

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