Variant report

Variant	rs3798740
Chromosome Location	chr6:11207687-11207688
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:11206545..11209352-chr6:11211717..11213636,2	K562	blood:
2	chr6:11206157..11210739-chr6:11227507..11231085,4	MCF-7	breast:
3	chr6:11172182..11173725-chr6:11207224..11208929,2	MCF-7	breast:
4	chr6:11207563..11208073-chr6:11344240..11345008,2	MCF-7	breast:
5	chr6:11207669..11210620-chr6:11314180..11315786,2	MCF-7	breast:
6	chr6:11206149..11208479-chr6:11352023..11353648,2	MCF-7	breast:
7	chr6:11206718..11208239-chr6:11210630..11212261,2	MCF-7	breast:
8	chr6:11197493..11200396-chr6:11205565..11209405,4	MCF-7	breast:
9	chr6:11199052..11200788-chr6:11207235..11209981,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000247925	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12215094	0.81[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs2034	0.87[ASN][1000 genomes]
rs3734402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3756966	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3778169	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798733	0.81[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798734	0.81[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798736	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798743	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6912916	0.81[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6915811	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928520	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937575	0.81[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs726230	0.81[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs9295813	0.81[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11197000-11211000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:11197000-11211200	Genic enhancers	HepG2	liver
3	chr6:11199400-11212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:11201000-11208600	Genic enhancers	Fetal Thymus	thymus
5	chr6:11201600-11207800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:11201600-11209600	Weak transcription	Fetal Brain Female	brain
7	chr6:11201600-11211000	Weak transcription	Gastric	stomach
8	chr6:11201800-11213000	Weak transcription	Esophagus	oesophagus
9	chr6:11203200-11208000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:11203400-11209800	Weak transcription	Spleen	Spleen
11	chr6:11203600-11208400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:11203800-11209000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:11203800-11210200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:11203800-11213200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:11203800-11213400	Weak transcription	Brain Germinal Matrix	brain
16	chr6:11204000-11207800	Weak transcription	Small Intestine	intestine
17	chr6:11204000-11208600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:11204000-11208600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:11204000-11208800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:11204000-11209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:11204000-11209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:11204000-11210600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:11204000-11211000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:11204200-11207800	Weak transcription	Aorta	Aorta
25	chr6:11204200-11208200	Weak transcription	Left Ventricle	heart
26	chr6:11204200-11208800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:11204200-11209600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:11204200-11209800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:11204200-11210000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:11204200-11211000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:11204200-11213600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:11204200-11213800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:11204200-11222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:11204400-11208800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:11204600-11208600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:11204800-11210800	Enhancers	Fetal Heart	heart
37	chr6:11205000-11208200	Enhancers	Fetal Lung	lung
38	chr6:11205200-11208000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:11205200-11215400	Genic enhancers	NH-A	brain
40	chr6:11205200-11217800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:11205400-11208200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:11205400-11209600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:11205600-11208200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:11205600-11208400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr6:11205800-11209400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:11206000-11207800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:11206000-11208000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:11206200-11207800	Weak transcription	Right Atrium	heart
49	chr6:11206200-11208000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:11206200-11208200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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