Variant report

Variant	rs12086884
Chromosome Location	chr1:192996357-192996358
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:192995040..192997652-chr1:192998864..193001424,2	MCF-7	breast:
2	chr1:192995746..192997937-chr1:192999203..193000719,2	K562	blood:
3	chr1:192996026..192997937-chr1:192998425..193000719,2	K562	blood:
4	chr1:192995490..192998261-chr1:193001490..193003087,2	K562	blood:
5	chr1:192995946..192996514-chr15:83878116..83878651,2	MCF-7	breast:
6	chr1:192996006..192999093-chr1:193026171..193028166,3	K562	blood:
7	chr1:192993820..193002591-chr1:193021038..193030016,12	K562	blood:

Variant related genes	Relation type
ENSG00000116747	Chromatin interaction
ENSG00000116750	Chromatin interaction
ENSG00000238754	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10494674	0.87[CHB][hapmap];0.96[JPT][hapmap];0.81[ASN][1000 genomes]
rs10732293	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10733078	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs10737620	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10737621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10737622	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10754044	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10754046	0.81[ASN][1000 genomes]
rs10754047	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10754048	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10754049	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10754052	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10801167	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs10801174	0.92[ASN][1000 genomes]
rs10801175	0.90[ASN][1000 genomes]
rs10801177	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10801178	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10801179	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10801183	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10801184	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10801187	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10801189	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10921304	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10921305	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10921308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10921310	0.92[ASN][1000 genomes]
rs10921312	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10921313	0.92[ASN][1000 genomes]
rs10921317	0.81[ASN][1000 genomes]
rs10921318	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10921319	0.81[ASN][1000 genomes]
rs10921323	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10921325	0.90[JPT][hapmap]
rs10921326	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11577299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11583763	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12090626	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12126529	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12137318	0.81[ASN][1000 genomes]
rs12141392	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145057	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs12410213	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12735445	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325197	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1539724	0.90[JPT][hapmap]
rs1555555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890660	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2181408	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2182106	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2186016	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2275444	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2370028	0.81[ASN][1000 genomes]
rs2370029	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2370079	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2370081	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753948	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806351	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs3818865	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820417	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3945872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4450000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4466634	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4657744	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4657840	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657842	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4657843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4657845	0.92[ASN][1000 genomes]
rs4657846	0.83[ASN][1000 genomes]
rs4657847	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs4657848	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4658079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6428151	0.81[ASN][1000 genomes]
rs6428152	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6428154	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6428156	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6661522	0.86[CHB][hapmap]
rs6663431	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6665069	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6665666	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6671237	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6672649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673271	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6675833	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6676322	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6676416	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6676878	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6680224	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6692342	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6692805	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697079	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6703727	0.92[ASN][1000 genomes]
rs7514072	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs7518792	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7519242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7534257	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7542466	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547615	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs7553247	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs912070	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs912071	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9427838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9783104	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv3966	chr1:192976457-193004886	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192963800-193012400	Weak transcription	NHEK	skin
2	chr1:192963800-193019600	Weak transcription	Ovary	ovary
3	chr1:192968000-193009400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:192968000-193012400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:192968000-193019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:192977600-193005200	Weak transcription	A549	lung
7	chr1:192979200-193025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:192981400-193026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:192982400-192996400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:192982600-193002400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:192983000-193017800	Weak transcription	HSMMtube	muscle
12	chr1:192983200-192996400	Weak transcription	Fetal Stomach	stomach
13	chr1:192983200-193000000	Weak transcription	Right Ventricle	heart
14	chr1:192983200-193012800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:192983200-193018000	Weak transcription	Pancreas	Pancrea
16	chr1:192983200-193023600	Weak transcription	Psoas Muscle	Psoas
17	chr1:192983200-193027800	Weak transcription	Aorta	Aorta
18	chr1:192984000-192997600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:192984000-192998200	Weak transcription	NHDF-Ad	bronchial
20	chr1:192984200-193026600	Weak transcription	NHLF	lung
21	chr1:192984400-193026400	Weak transcription	HUVEC	blood vessel
22	chr1:192984800-193025800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:192986200-193012000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:192987000-193009200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:192987400-193026200	Weak transcription	Fetal Kidney	kidney
26	chr1:192988600-192997800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:192988600-193008400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:192988800-192997200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:192988800-192997400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:192988800-193006000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:192988800-193012600	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:192989000-192998800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:192989200-192996600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:192989400-192997400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:192989800-192998400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:192989800-193012600	Weak transcription	Spleen	Spleen
37	chr1:192990000-192997200	Strong transcription	Fetal Thymus	thymus
38	chr1:192990400-192998600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:192990400-192998800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:192990400-192998800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:192990600-192999600	Strong transcription	Dnd41	blood
42	chr1:192990800-193012800	Weak transcription	Fetal Brain Female	brain
43	chr1:192991200-192996600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:192991200-192997200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:192991200-193014400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:192991400-193012600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:192991400-193018000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:192991600-192997000	Weak transcription	HMEC	breast
49	chr1:192991600-193009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:192991600-193018000	Weak transcription	H9 Cell Line	embryonic stem cell

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