Variant report

Variant	rs2544860
Chromosome Location	chr5:154222557-154222558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154131390..154134045-chr5:154222442..154224295,2	MCF-7	breast:
2	chr5:154213002..154215551-chr5:154220667..154225908,5	MCF-7	breast:
3	chr5:154216928..154219403-chr5:154221104..154224091,2	MCF-7	breast:
4	chr5:154218437..154223942-chr5:154231920..154239988,10	K562	blood:
5	chr5:154209195..154209843-chr5:154222467..154223169,2	MCF-7	breast:
6	chr5:154208072..154211550-chr5:154221062..154224039,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155508	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000263361	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1035368	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11167705	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187921	0.85[CHB][hapmap]
rs12188828	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12300	0.86[JPT][hapmap]
rs1233078	0.91[CEU][hapmap];0.82[YRI][hapmap]
rs158134	0.85[ASN][1000 genomes]
rs17116421	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17116433	0.86[CHB][hapmap]
rs17116442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17116534	0.86[JPT][hapmap]
rs180846	0.86[CHB][hapmap]
rs1974776	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1974777	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2042168	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2112223	0.86[JPT][hapmap]
rs2161128	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2258437	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2431184	0.81[ASN][1000 genomes]
rs2544866	0.81[ASN][1000 genomes]
rs2544875	0.84[ASN][1000 genomes]
rs2544880	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs255529	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644743	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2644744	0.86[JPT][hapmap]
rs2688186	0.84[ASN][1000 genomes]
rs2688188	0.84[ASN][1000 genomes]
rs2688191	0.84[ASN][1000 genomes]
rs2688193	0.84[ASN][1000 genomes]
rs2688198	0.86[JPT][hapmap]
rs2688200	0.83[ASN][1000 genomes]
rs2688201	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2688208	0.86[JPT][hapmap]
rs286623	0.81[EUR][1000 genomes]
rs286624	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32427	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs348739	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs348748	0.86[CHB][hapmap]
rs348749	0.85[CHB][hapmap]
rs348750	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs348751	0.81[ASN][1000 genomes]
rs348752	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs348754	0.81[ASN][1000 genomes]
rs39614	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4354100	0.81[ASN][1000 genomes]
rs454161	0.81[ASN][1000 genomes]
rs4958771	0.81[ASN][1000 genomes]
rs56374414	0.81[ASN][1000 genomes]
rs58415346	0.81[ASN][1000 genomes]
rs59525998	0.81[ASN][1000 genomes]
rs6580122	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6873483	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6879277	0.81[ASN][1000 genomes]
rs6884416	0.84[ASN][1000 genomes]
rs702742	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73276742	0.81[ASN][1000 genomes]
rs73280705	0.81[ASN][1000 genomes]
rs816717	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs816718	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs816720	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs816734	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs816747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs960499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
2	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
3	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:154210200-154229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154210800-154229000	Weak transcription	Fetal Kidney	kidney
6	chr5:154210800-154229800	Weak transcription	Fetal Thymus	thymus
7	chr5:154211400-154228800	Weak transcription	Fetal Brain Female	brain
8	chr5:154211400-154229400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:154211400-154229400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:154211400-154229800	Weak transcription	Pancreas	Pancrea
11	chr5:154211400-154235800	Weak transcription	Dnd41	blood
12	chr5:154211800-154222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:154211800-154229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:154211800-154229200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:154212400-154229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:154212600-154229400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:154214600-154229200	Weak transcription	Esophagus	oesophagus
18	chr5:154214600-154229400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:154214600-154229800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:154214800-154229400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:154214800-154230000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:154214800-154236400	Weak transcription	GM12878-XiMat	blood
23	chr5:154215000-154222600	Weak transcription	Stomach Mucosa	stomach
24	chr5:154215000-154224400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:154215000-154224400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:154215000-154229000	Weak transcription	NHLF	lung
27	chr5:154215000-154229800	Weak transcription	Placenta	Placenta
28	chr5:154215200-154222600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:154215200-154228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:154215200-154228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:154215200-154229200	Weak transcription	Colonic Mucosa	Colon
32	chr5:154215200-154236400	Weak transcription	A549	lung
33	chr5:154215800-154223000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:154215800-154228800	Weak transcription	Osteobl	bone
35	chr5:154215800-154229400	Weak transcription	HMEC	breast
36	chr5:154215800-154229800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:154216000-154227800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:154216000-154229000	Weak transcription	NHDF-Ad	bronchial
39	chr5:154216000-154229800	Weak transcription	NHEK	skin
40	chr5:154216200-154222600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:154216200-154222800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:154216800-154224000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:154217600-154222600	Weak transcription	Brain Anterior Caudate	brain
44	chr5:154217600-154228800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:154217600-154229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:154217600-154229800	Weak transcription	Gastric	stomach
47	chr5:154217800-154222600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:154217800-154222600	Weak transcription	Small Intestine	intestine
49	chr5:154217800-154224400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:154217800-154224400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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