Variant report

Variant	rs4671954
Chromosome Location	chr2:54772104-54772105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54771500..54773380-chr2:54779555..54782261,2	MCF-7	breast:
2	chr2:54770128..54773516-chr2:54775238..54777528,3	MCF-7	breast:
3	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:
4	chr2:54764232..54766337-chr2:54769153..54772806,3	K562	blood:

Variant related genes	Relation type
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10165490	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11892788	0.89[ASN][1000 genomes]
rs11898012	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104998	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12105792	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617036	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016942	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13399435	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1367295	0.80[EUR][1000 genomes]
rs17344044	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17344072	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17521078	0.82[ASN][1000 genomes]
rs1802889	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1864493	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4233954	0.96[EUR][1000 genomes]
rs4514918	0.89[EUR][1000 genomes]
rs4592889	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671221	0.82[ASN][1000 genomes]
rs4671222	0.87[ASN][1000 genomes]
rs4671225	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671226	0.81[EUR][1000 genomes]
rs4671945	0.82[ASN][1000 genomes]
rs4671949	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671950	0.96[EUR][1000 genomes]
rs4671951	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671953	0.90[EUR][1000 genomes]
rs4671955	0.85[ASN][1000 genomes]
rs4671956	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671960	0.91[EUR][1000 genomes]
rs4671961	0.91[EUR][1000 genomes]
rs4990319	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545411	0.82[ASN][1000 genomes]
rs6545413	0.83[ASN][1000 genomes]
rs6545414	0.83[ASN][1000 genomes]
rs6545418	0.80[ASN][1000 genomes]
rs6545419	0.82[ASN][1000 genomes]
rs6545420	0.89[EUR][1000 genomes]
rs6545421	0.87[EUR][1000 genomes]
rs6545427	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545429	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704769	0.85[EUR][1000 genomes]
rs6729826	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6746016	0.84[ASN][1000 genomes]
rs6761369	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6761398	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558950	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7563706	0.81[ASN][1000 genomes]
rs7589236	0.82[EUR][1000 genomes];0.95[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
8	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:54762200-54772800	Weak transcription	Aorta	Aorta
10	chr2:54762200-54772800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:54762400-54772600	Weak transcription	Liver	Liver
13	chr2:54762800-54772600	Weak transcription	NHDF-Ad	bronchial
14	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:54763200-54772600	Weak transcription	NHLF	lung
16	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:54764400-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:54764600-54772600	Weak transcription	Osteobl	bone
19	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
20	chr2:54766200-54772800	Weak transcription	Small Intestine	intestine
21	chr2:54767400-54772600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:54767400-54772800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:54767800-54772600	Weak transcription	HUVEC	blood vessel
24	chr2:54767800-54772600	Weak transcription	NH-A	brain
25	chr2:54767800-54773000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:54768200-54772600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:54768400-54772800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:54768400-54773000	Weak transcription	Fetal Lung	lung
30	chr2:54768400-54773600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:54768400-54775800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:54768600-54772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54768800-54772800	Weak transcription	HSMM	muscle
34	chr2:54768800-54772800	Weak transcription	HSMMtube	muscle
35	chr2:54769400-54772400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54769800-54772600	Enhancers	HepG2	liver
37	chr2:54769800-54772800	Weak transcription	Spleen	Spleen
38	chr2:54769800-54775400	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:54769800-54775600	Weak transcription	Fetal Stomach	stomach
40	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
41	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
42	chr2:54770200-54772600	Weak transcription	Fetal Heart	heart
43	chr2:54770400-54772600	Weak transcription	Brain Substantia Nigra	brain
44	chr2:54770400-54772800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:54770400-54772800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:54770400-54772800	Weak transcription	Right Ventricle	heart
47	chr2:54770400-54773000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:54770400-54775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:54770400-54775400	Weak transcription	Lung	lung
50	chr2:54770400-54776800	Weak transcription	Fetal Muscle Trunk	muscle

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