Variant report

Variant	rs2054745
Chromosome Location	chr3:196345987-196345988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196344291..196346990-chr3:196361861..196363448,2	K562	blood:
2	chr3:196344681..196346820-chr3:196413702..196415608,2	MCF-7	breast:
3	chr3:196345698..196350992-chr3:196355970..196361124,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1552321	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1684456	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs1825471	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4346577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4591526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779465	0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs7426670	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824819	0.83[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196337000-196347000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:196337200-196347000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:196339000-196346000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:196339200-196346200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:196339400-196346000	Weak transcription	Right Atrium	heart
6	chr3:196339600-196346000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:196339600-196346000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:196339600-196346200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:196339600-196346800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:196339600-196347000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:196339600-196347000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:196339600-196347000	Weak transcription	Lung	lung
13	chr3:196339600-196354800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:196339800-196346000	Weak transcription	Adipose Nuclei	Adipose
15	chr3:196339800-196346000	Weak transcription	Placenta	Placenta
16	chr3:196339800-196351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:196340000-196346000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:196340000-196346000	Weak transcription	K562	blood
19	chr3:196340000-196347200	Weak transcription	Spleen	Spleen
20	chr3:196340600-196350200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:196340800-196346000	Weak transcription	HUVEC	blood vessel
22	chr3:196340800-196346800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:196341000-196346200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:196342400-196347200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:196343000-196349200	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:196343400-196346000	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:196343400-196351000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:196344200-196347600	Enhancers	Fetal Intestine Small	intestine
29	chr3:196344400-196346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:196344400-196346800	Weak transcription	GM12878-XiMat	blood
31	chr3:196344600-196346000	Weak transcription	HepG2	liver
32	chr3:196344600-196346800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:196344600-196350200	Weak transcription	Primary T cells from cord blood	blood
34	chr3:196344600-196351000	Weak transcription	Thymus	Thymus
35	chr3:196345200-196346000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:196345200-196346000	Weak transcription	Dnd41	blood
37	chr3:196345400-196351200	Enhancers	Fetal Thymus	thymus
38	chr3:196345600-196346200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:196345600-196347000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:196345600-196347600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:196345600-196347600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:196345600-196347800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:196345800-196346600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr3:196345800-196346600	Enhancers	Brain Cingulate Gyrus	brain
45	chr3:196345800-196347000	Enhancers	Colon Smooth Muscle	Colon
46	chr3:196345800-196347200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr3:196345800-196347200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:196345800-196347600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:196345800-196347600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:196345800-196347800	Enhancers	Rectal Smooth Muscle	rectum

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