Variant report

Variant	rs12193557
Chromosome Location	chr6:27435944-27435945
allele	C/T
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	chr6:27434557..27436351-chr6:27436388..27438745,2	MCF-7	breast:
2	chr6:27434893..27436769-chr6:27444407..27446972,3	K562	blood:
3	chr6:27429105..27431185-chr6:27434916..27437111,2	K562	blood:
4	chr6:27427630..27430892-chr6:27435526..27437127,4	K562	blood:
5	chr6:27372759..27375029-chr6:27434389..27436500,2	K562	blood:
6	chr6:27417734..27419835-chr6:27434230..27437154,2	K562	blood:
7	chr6:27435057..27436916-chr6:27758569..27760207,2	K562	blood:
8	chr6:27431405..27433354-chr6:27435095..27436634,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271755	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456051	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10456355	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12189640	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12191373	1.00[CEU][hapmap]
rs12191414	0.85[CEU][hapmap]
rs12191649	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12192560	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12194341	1.00[AMR][1000 genomes]
rs12194842	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12195783	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12196452	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12196970	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12199685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12199806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12202956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12204953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12205044	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12209174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12209905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12211931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12212348	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12212389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12212632	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12213471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12213533	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12215289	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12215353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12215386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12215878	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12374607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12374649	1.00[AMR][1000 genomes]
rs56099947	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57075114	0.83[EUR][1000 genomes]
rs60888769	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62617138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71546544	0.84[AMR][1000 genomes]
rs72839448	1.00[AFR][1000 genomes]
rs72839468	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72839469	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72839470	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72839471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72839474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72839479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72841397	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72841398	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72841399	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72841400	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72843151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72843177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72843191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72845006	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845008	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845011	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845012	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845025	0.84[AMR][1000 genomes]
rs72845027	0.84[AMR][1000 genomes]
rs72845028	0.84[AMR][1000 genomes]
rs72845030	0.84[AMR][1000 genomes]
rs72845031	0.84[AMR][1000 genomes]
rs72845042	0.84[AMR][1000 genomes]
rs72845044	0.84[AMR][1000 genomes]
rs72845050	0.84[AMR][1000 genomes]
rs72845208	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72845232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9348759	0.80[CEU][hapmap]
rs9348763	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9368500	0.80[CEU][hapmap]
rs9368509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9379975	0.80[CEU][hapmap];0.86[AMR][1000 genomes]
rs9393802	0.85[CEU][hapmap]
rs9393814	1.00[AFR][1000 genomes];1.00[AMR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv883508	chr6:27434220-27455625	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27415400-27438600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27424000-27439800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27425000-27438800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:27425400-27438400	Weak transcription	Fetal Brain Male	brain
6	chr6:27425600-27439400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:27426400-27438200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr6:27426600-27438200	Strong transcription	Fetal Thymus	thymus
9	chr6:27427800-27440000	Weak transcription	Esophagus	oesophagus
10	chr6:27428400-27438800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:27428800-27437800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:27428800-27439800	Weak transcription	Pancreas	Pancrea
13	chr6:27429200-27437400	Weak transcription	Small Intestine	intestine
14	chr6:27429400-27437200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr6:27429400-27439000	Weak transcription	Stomach Mucosa	stomach
16	chr6:27429600-27437800	Weak transcription	Fetal Heart	heart
17	chr6:27429600-27439800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:27429600-27440000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:27429600-27440000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:27429800-27436200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:27429800-27439000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:27429800-27439800	Weak transcription	Colonic Mucosa	Colon
23	chr6:27430000-27436200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr6:27430000-27438400	Weak transcription	HepG2	liver
25	chr6:27430000-27438800	Weak transcription	Brain Angular Gyrus	brain
26	chr6:27430400-27436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:27430800-27437000	Strong transcription	Fetal Lung	lung
28	chr6:27431200-27436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:27431200-27437600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:27431200-27437800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr6:27431200-27438000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:27431400-27439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:27431600-27436800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:27431600-27437000	Strong transcription	NHDF-Ad	bronchial
35	chr6:27431800-27436000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:27431800-27438800	Strong transcription	HSMM	muscle
37	chr6:27432400-27436200	Weak transcription	Hela-S3	cervix
38	chr6:27432400-27436600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:27432800-27438800	Weak transcription	NHLF	lung
40	chr6:27433200-27438400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:27433400-27436000	Strong transcription	HSMMtube	muscle
42	chr6:27433400-27436000	Strong transcription	K562	blood
43	chr6:27433400-27436000	Strong transcription	Osteobl	bone
44	chr6:27433400-27436200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:27433400-27436200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:27433400-27437000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:27433400-27437000	Strong transcription	Placenta	Placenta
48	chr6:27433400-27437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:27433400-27437600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:27433400-27437800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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