Variant report

Variant	rs12188498
Chromosome Location	chr5:154164704-154164705
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	chr5:154164555..154166068-chr5:154237467..154239293,2	K562	blood:
2	chr5:154133706..154138034-chr5:154163446..154168926,6	MCF-7	breast:
3	chr5:154158451..154160663-chr5:154164358..154166909,3	MCF-7	breast:
4	chr5:154135295..154138136-chr5:154163169..154165324,3	MCF-7	breast:
5	chr5:154163381..154166073-chr5:154170171..154172796,2	MCF-7	breast:
6	chr5:154164286..154166504-chr5:154178715..154180679,2	MCF-7	breast:
7	chr5:154161718..154166122-chr5:154172267..154174755,4	MCF-7	breast:
8	chr5:154163355..154165519-chr5:154191104..154193464,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186480	0.86[ASN][1000 genomes]
rs12186610	0.88[EUR][1000 genomes]
rs12187572	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187890	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12187921	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12187934	0.82[ASN][1000 genomes]
rs12187974	0.86[ASN][1000 genomes]
rs12188149	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12188906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189508	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17096232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17116417	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116669	0.82[ASN][1000 genomes]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2047305	1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2544880	1.00[TSI][hapmap]
rs2544884	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs2688198	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.86[ASN][1000 genomes]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs348752	1.00[TSI][hapmap]
rs3776984	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39614	1.00[TSI][hapmap]
rs4452598	0.89[EUR][1000 genomes]
rs4626377	0.89[EUR][1000 genomes]
rs55692274	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56773390	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56895891	0.86[ASN][1000 genomes]
rs61145644	0.82[ASN][1000 genomes]
rs6580123	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871813	0.82[ASN][1000 genomes]
rs6895588	0.82[ASN][1000 genomes]
rs6895702	0.82[ASN][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs702742	1.00[TSI][hapmap]
rs73806917	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807206	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807207	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807213	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807216	0.82[ASN][1000 genomes]
rs73809507	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709899	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	1.00[CHB][hapmap];0.95[TSI][hapmap]
rs816720	1.00[TSI][hapmap]

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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154151600-154171200	Weak transcription	Fetal Brain Male	brain
2	chr5:154152600-154168200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr5:154152600-154168400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr5:154157800-154168000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:154157800-154168200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr5:154157800-154168200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:154157800-154168400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr5:154158000-154168200	Enhancers	Left Ventricle	heart
9	chr5:154158000-154168400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:154158200-154168200	Enhancers	Spleen	Spleen
11	chr5:154158800-154168200	Enhancers	Pancreas	Pancrea
12	chr5:154159000-154166800	Weak transcription	HUVEC	blood vessel
13	chr5:154159000-154168000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr5:154159400-154167800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr5:154159400-154168200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr5:154159600-154168200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:154159800-154167400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:154159800-154168400	Strong transcription	Dnd41	blood
19	chr5:154160000-154164800	Weak transcription	Hela-S3	cervix
20	chr5:154160400-154168200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr5:154160600-154165000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr5:154160600-154165000	Enhancers	Small Intestine	intestine
23	chr5:154161200-154165200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:154161200-154167600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:154161200-154168000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:154161200-154168000	Enhancers	Stomach Mucosa	stomach
27	chr5:154161200-154168400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:154161200-154168600	Enhancers	Fetal Heart	heart
29	chr5:154161400-154164800	Enhancers	Adipose Nuclei	Adipose
30	chr5:154161400-154165000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:154161400-154165200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:154161400-154165600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr5:154161400-154166000	Enhancers	Brain Angular Gyrus	brain
34	chr5:154161400-154166200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:154161400-154166400	Enhancers	Fetal Intestine Large	intestine
36	chr5:154161400-154166800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:154161400-154167600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr5:154161400-154168000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:154161400-154168200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:154161400-154168200	Enhancers	Brain Anterior Caudate	brain
41	chr5:154161400-154168200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:154161400-154168200	Enhancers	Ovary	ovary
43	chr5:154161400-154168600	Enhancers	Psoas Muscle	Psoas
44	chr5:154161600-154164800	Enhancers	Fetal Muscle Leg	muscle
45	chr5:154161600-154165000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:154161600-154165000	Enhancers	Brain Substantia Nigra	brain
47	chr5:154161600-154165600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr5:154161600-154166800	Enhancers	Osteobl	bone
49	chr5:154161600-154167400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:154161600-154168000	Enhancers	Brain Hippocampus Middle	brain

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