Variant report

Variant	rs13978
Chromosome Location	chr6:26599043-26599044
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26155821..26161666-chr6:26595746..26599191,6	K562	blood:
2	chr6:26123945..26125914-chr6:26596676..26599538,2	MCF-7	breast:
3	chr6:26594524..26600977-chr6:27096034..27104390,19	K562	blood:
4	chr6:26586123..26588537-chr6:26597287..26599098,2	K562	blood:
5	chr6:26597702..26602573-chr6:27112472..27116781,7	MCF-7	breast:
6	chr6:26593362..26600987-chr6:27097692..27106488,18	K562	blood:
7	chr6:26500256..26501997-chr6:26596237..26599100,2	K562	blood:
8	chr6:26595623..26599966-chr6:27100615..27102925,4	MCF-7	breast:
9	chr6:26598518..26601187-chr6:27104748..27107582,2	MCF-7	breast:
10	chr6:26593150..26599498-chr6:27112360..27118946,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000158373	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000124557	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13437351	1.00[JPT][hapmap]
rs2281027	1.00[JPT][hapmap]
rs3734541	1.00[JPT][hapmap]
rs3846842	1.00[JPT][hapmap]
rs3857549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57538609	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57768474	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59034876	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6456720	1.00[JPT][hapmap]
rs6456725	1.00[JPT][hapmap]
rs6456726	1.00[JPT][hapmap]
rs6901118	1.00[JPT][hapmap]
rs6902081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6907857	1.00[JPT][hapmap]
rs6910849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6910871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910921	1.00[JPT][hapmap]
rs6910993	1.00[JPT][hapmap]
rs6911470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs6911476	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929846	1.00[JPT][hapmap]
rs73397148	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7751645	1.00[JPT][hapmap]
rs7769926	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7773913	1.00[JPT][hapmap]
rs9295692	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9295700	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9461252	1.00[JPT][hapmap]
rs9461253	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9461254	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9461277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467753	1.00[JPT][hapmap]
rs9467757	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9467759	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs9467760	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9467761	1.00[JPT][hapmap]
rs9467768	1.00[JPT][hapmap]
rs9467771	1.00[JPT][hapmap]
rs9467788	1.00[JPT][hapmap]
rs9467803	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467816	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9467818	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9467824	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9467838	0.82[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26598000-26604800	Weak transcription	Aorta	Aorta
2	chr6:26598000-26606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:26598200-26599200	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr6:26598200-26599200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:26598200-26599200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:26598200-26599200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:26598200-26599200	Genic enhancers	Thymus	Thymus
8	chr6:26598200-26599200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
9	chr6:26598200-26607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:26598400-26599200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:26598400-26599200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:26598400-26599200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:26598400-26599200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:26598400-26599400	Strong transcription	Fetal Intestine Small	intestine
15	chr6:26598400-26600000	Strong transcription	Fetal Stomach	stomach
16	chr6:26598400-26600200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:26598400-26600200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:26598400-26600400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:26598400-26600400	Strong transcription	A549	lung
20	chr6:26598400-26600600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:26598400-26601000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:26598400-26601200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:26598600-26599200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:26598600-26599200	Genic enhancers	Primary hematopoietic stem cells	blood
25	chr6:26598600-26599200	Genic enhancers	Pancreas	Pancrea
26	chr6:26598600-26599400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:26598600-26599400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:26598600-26599400	Strong transcription	Right Ventricle	heart
29	chr6:26598600-26599400	Strong transcription	Small Intestine	intestine
30	chr6:26598600-26599600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:26598600-26599600	Strong transcription	Colonic Mucosa	Colon
32	chr6:26598600-26599800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:26598600-26599800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:26598600-26600000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr6:26598600-26600000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:26598600-26600000	Strong transcription	HSMMtube	muscle
37	chr6:26598600-26600000	Strong transcription	HUVEC	blood vessel
38	chr6:26598600-26600000	Strong transcription	NHLF	lung
39	chr6:26598600-26600200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:26598600-26600200	Strong transcription	Brain Angular Gyrus	brain
41	chr6:26598600-26600200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:26598600-26600400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:26598600-26600400	Strong transcription	Colon Smooth Muscle	Colon
44	chr6:26598600-26600400	Strong transcription	Ovary	ovary
45	chr6:26598600-26600600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:26598600-26600600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:26598600-26600600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:26598600-26600600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:26598600-26600800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:26598600-26600800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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