Variant report

Variant	rs2999550
Chromosome Location	chr1:152005482-152005483
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
2	chr1:152003508..152006016-chr3:64240085..64241940,2	MCF-7	breast:
3	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
4	chr1:151997592..152000078-chr1:152004564..152007278,3	K562	blood:
5	chr1:151904319..151906408-chr1:152003368..152007237,3	MCF-7	breast:
6	chr1:152004872..152007775-chr21:40685504..40687416,2	MCF-7	breast:
7	chr1:152003216..152005599-chr1:152046745..152048519,2	MCF-7	breast:
8	chr1:152004874..152008437-chr1:152153479..152155850,3	MCF-7	breast:
9	chr1:152004094..152009269-chr1:152022985..152027910,7	K562	blood:
10	chr1:152005022..152006958-chr1:152156350..152158073,2	MCF-7	breast:
11	chr1:151978047..151980074-chr1:152004028..152006807,2	K562	blood:
12	chr1:152004903..152005861-chr10:37909534..37910318,2	MCF-7	breast:
13	chr1:152003076..152005594-chr1:152022985..152024993,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12123975	0.80[EUR][1000 genomes]
rs2999547	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2999552	0.90[ASN][1000 genomes]
rs2999555	0.84[ASN][1000 genomes]
rs2999559	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007671	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007674	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007676	0.90[ASN][1000 genomes]
rs3007677	0.90[ASN][1000 genomes]
rs3007679	0.84[ASN][1000 genomes]
rs3122300	0.90[ASN][1000 genomes]
rs3122302	0.82[ASN][1000 genomes]
rs3811422	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:152001600-152006000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:152001800-152007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:152002000-152007400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:152002600-152005600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:152002600-152005800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:152002600-152005800	Strong transcription	Fetal Thymus	thymus
10	chr1:152002600-152006400	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:152002800-152006200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:152002800-152006800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:152003000-152006000	Strong transcription	Fetal Intestine Small	intestine
14	chr1:152003000-152006400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:152003200-152005600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:152003200-152005600	Strong transcription	Adipose Nuclei	Adipose
17	chr1:152003200-152005600	Strong transcription	Thymus	Thymus
18	chr1:152003200-152006000	Strong transcription	HUVEC	blood vessel
19	chr1:152003200-152006200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr1:152003200-152006400	Genic enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:152003200-152006400	Strong transcription	HSMMtube	muscle
22	chr1:152003200-152006600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:152003400-152005800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:152003400-152006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:152003400-152006000	Strong transcription	Osteobl	bone
26	chr1:152003400-152006200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:152003400-152006400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:152003400-152006400	Strong transcription	Lung	lung
29	chr1:152003400-152006400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:152003400-152006400	Strong transcription	NH-A	brain
31	chr1:152003400-152006800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:152003600-152006400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:152003600-152006600	Strong transcription	Fetal Stomach	stomach
34	chr1:152003800-152005600	Strong transcription	Hela-S3	cervix
35	chr1:152003800-152006400	Strong transcription	HSMM	muscle
36	chr1:152004000-152005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:152004000-152005800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:152004000-152005800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:152004000-152006000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:152004000-152006000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:152004000-152006000	Strong transcription	Liver	Liver
42	chr1:152004000-152006000	Strong transcription	Fetal Kidney	kidney
43	chr1:152004000-152006000	Strong transcription	NHLF	lung
44	chr1:152004000-152006200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:152004000-152006200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:152004000-152006200	Strong transcription	Aorta	Aorta
47	chr1:152004000-152006200	Strong transcription	Psoas Muscle	Psoas
48	chr1:152004000-152006200	Strong transcription	Small Intestine	intestine
49	chr1:152004000-152006400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:152004000-152006400	Strong transcription	Rectal Smooth Muscle	rectum

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