Variant report

Variant	rs1335536
Chromosome Location	chr6:79942562-79942563
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:79942454-79942803	HepG2	liver:	n/a	chr6:79942616-79942625
2	POLR2A	chr6:79942550-79944754	GM12878	blood:	n/a	n/a
3	RFX5	chr6:79942075-79945226	SK-N-SH	brain:	n/a	chr6:79944581-79944596
4	YY1	chr6:79942413-79942639	H1-hESC	embryonic stem cell:	n/a	chr6:79942504-79942512 chr6:79942503-79942515 chr6:79942493-79942515

No.	Distal block	Cell Line	Cell type
1	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
2	chr6:79763581..79765481-chr6:79941505..79943028,2	K562	blood:
3	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

Variant related genes	Relation type
HMGN3-AS1	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484945	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16890581	1.00[EUR][1000 genomes]
rs196677	1.00[CEU][hapmap]
rs196711	1.00[EUR][1000 genomes]
rs196718	1.00[EUR][1000 genomes]
rs196719	1.00[EUR][1000 genomes]
rs35686657	1.00[EUR][1000 genomes]
rs55654065	1.00[EUR][1000 genomes]
rs55779333	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55786726	1.00[EUR][1000 genomes]
rs56125439	1.00[EUR][1000 genomes]
rs56177348	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56857693	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56926933	1.00[EUR][1000 genomes]
rs57810626	1.00[EUR][1000 genomes]
rs58284219	1.00[EUR][1000 genomes]
rs59392118	1.00[EUR][1000 genomes]
rs60420555	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61411441	1.00[EUR][1000 genomes]
rs6904575	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917206	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73466210	1.00[EUR][1000 genomes]
rs73466218	1.00[EUR][1000 genomes]
rs73466221	1.00[EUR][1000 genomes]
rs73466224	1.00[EUR][1000 genomes]
rs73466240	1.00[EUR][1000 genomes]
rs73466263	1.00[EUR][1000 genomes]
rs73466271	1.00[EUR][1000 genomes]
rs73466273	1.00[EUR][1000 genomes]
rs73466290	1.00[EUR][1000 genomes]
rs73764092	1.00[EUR][1000 genomes]
rs73767528	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7753588	1.00[EUR][1000 genomes]
rs7762406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79907400-79942800	Weak transcription	HSMM	muscle
2	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:79925800-79942800	Weak transcription	Liver	Liver
9	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
13	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine
15	chr6:79936200-79943000	Weak transcription	Psoas Muscle	Psoas
16	chr6:79936200-79943200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:79936800-79942800	Weak transcription	Fetal Kidney	kidney
18	chr6:79937400-79942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:79939000-79942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:79940200-79942800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:79940200-79942800	Weak transcription	HMEC	breast
22	chr6:79940400-79942800	Weak transcription	NHEK	skin
23	chr6:79940600-79942800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:79940600-79942800	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:79940800-79942800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:79940800-79942800	Enhancers	Brain Hippocampus Middle	brain
27	chr6:79940800-79942800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr6:79940800-79942800	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:79940800-79942800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:79940800-79943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr6:79941000-79942800	Enhancers	HepG2	liver
32	chr6:79941000-79943000	Enhancers	Fetal Heart	heart
33	chr6:79941200-79942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:79941200-79942800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:79941200-79943200	Weak transcription	Pancreas	Pancrea
36	chr6:79941400-79942600	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:79941400-79942800	Weak transcription	Fetal Lung	lung
38	chr6:79941400-79942800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:79941600-79942800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:79941600-79942800	Enhancers	Colon Smooth Muscle	Colon
41	chr6:79941600-79942800	Weak transcription	Thymus	Thymus
42	chr6:79941600-79943000	Enhancers	Fetal Intestine Small	intestine
43	chr6:79941600-79943000	Enhancers	Placenta	Placenta
44	chr6:79941600-79945000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:79941800-79942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:79941800-79942800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:79941800-79943000	Enhancers	Brain Angular Gyrus	brain
48	chr6:79941800-79943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:79942000-79942600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:79942000-79942600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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