Variant report

Variant	rs473504
Chromosome Location	chr2:234762272-234762273
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234761712..234762368-chr4:32022794..32023621,2	Hela-S3	cervix:
2	chr2:234399142..234401068-chr2:234759873..234762356,2	MCF-7	breast:
3	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:
4	chr2:234760939..234763453-chr2:235403879..235406192,2	K562	blood:
5	chr2:234759783..234762312-chr2:234875051..234877633,2	K562	blood:
6	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:
7	chr2:234387565..234390486-chr2:234761608..234763193,2	MCF-7	breast:
8	chr2:233739634..233741752-chr2:234762062..234763820,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction
ENSG00000144481	Chromatin interaction
ENSG00000188042	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10173569	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11562979	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11563228	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11563231	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13384575	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13384669	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13390819	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13398248	0.86[EUR][1000 genomes]
rs13403318	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13406453	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13406457	0.86[EUR][1000 genomes]
rs13410024	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13410032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13417465	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13427471	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17862903	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17862907	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17863825	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17863826	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17864729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17868368	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17868369	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs213556	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2173746	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2173747	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2530796	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2650888	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs494812	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs498680	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs498696	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs498786	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs498790	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs499703	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs501650	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs502321	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs506632	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs522389	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs529963	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531771	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs536265	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566529	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575194	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs577734	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs577782	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs577820	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs579327	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs581377	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs596509	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs598759	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs598760	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs606397	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611131	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs611169	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs611563	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs619351	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622954	0.82[AMR][1000 genomes]
rs625151	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs628138	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs657658	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs658054	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs658607	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs672831	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs686003	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs686007	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs686802	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs688677	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs693637	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers 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	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
3	chr2:234756600-234762600	Transcr. at gene 5' and 3'	A549	lung
4	chr2:234759000-234762600	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr2:234760400-234762400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:234760400-234762400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr2:234760400-234763000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:234760600-234762400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:234760600-234762400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
10	chr2:234760600-234762400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:234760600-234762400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:234760600-234762400	Flanking Active TSS	Osteobl	bone
13	chr2:234760600-234762600	Flanking Active TSS	HUVEC	blood vessel
14	chr2:234760800-234762400	Transcr. at gene 5' and 3'	K562	blood
15	chr2:234760800-234762800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:234760800-234762800	Flanking Active TSS	Thymus	Thymus
17	chr2:234760800-234763000	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr2:234761000-234762400	Weak transcription	Spleen	Spleen
19	chr2:234761000-234762600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:234761200-234762400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:234761200-234762800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr2:234761200-234763600	Active TSS	NHLF	lung
23	chr2:234761200-234764000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:234761400-234762400	Active TSS	Fetal Brain Female	brain
25	chr2:234761400-234763800	Active TSS	NHDF-Ad	bronchial
26	chr2:234761400-234764000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr2:234761600-234762800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr2:234761600-234762800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:234761600-234762800	Flanking Active TSS	Fetal Stomach	stomach
30	chr2:234761600-234763000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr2:234761600-234763600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:234761600-234763600	Active TSS	Hela-S3	cervix
33	chr2:234761600-234763800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr2:234761600-234763800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:234761600-234763800	Active TSS	Fetal Kidney	kidney
36	chr2:234761600-234763800	Active TSS	GM12878-XiMat	blood
37	chr2:234761800-234762400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:234761800-234762400	Flanking Active TSS	HMEC	breast
39	chr2:234761800-234762600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:234761800-234762600	Flanking Active TSS	Fetal Heart	heart
41	chr2:234761800-234762600	Flanking Active TSS	NH-A	brain
42	chr2:234761800-234762800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr2:234761800-234762800	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr2:234761800-234763000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr2:234761800-234763000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr2:234761800-234763400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:234761800-234763600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:234761800-234763800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:234761800-234763800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:234761800-234763800	Active TSS	Fetal Intestine Small	intestine

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