Variant report

Variant	rs11968469
Chromosome Location	chr6:27729951-27729952
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27598999..27601742-chr6:27728041..27730837,2	K562	blood:
2	chr6:27720750..27725347-chr6:27727186..27730834,4	MCF-7	breast:
3	chr6:27342508..27344098-chr6:27729808..27732720,2	K562	blood:
4	chr6:27729351..27732298-chr6:27734296..27736839,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2AI-1	chr6:27729282-27730265	ENSG00000248841
2	lnc-HIST1H2AI-1	chr6:27729504-27730863	XLOC_005221

No data

Variant related genes	Relation type
ENSG00000238648	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11966565	1.00[ASN][1000 genomes]
rs56002038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59199903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60339576	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901437	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906904	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6906980	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6908615	1.00[ASN][1000 genomes]
rs6915101	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938018	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384331	1.00[ASN][1000 genomes]
rs73389017	1.00[ASN][1000 genomes]
rs73389037	1.00[ASN][1000 genomes]
rs73389068	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742752	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468227	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	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
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27730200	Weak transcription	NHEK	skin
2	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
3	chr6:27726400-27733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:27726400-27738600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:27727200-27730200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:27729000-27730000	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:27729200-27730200	Active TSS	Fetal Brain Female	brain
8	chr6:27729200-27730600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr6:27729200-27730800	Active TSS	Primary B cells from cord blood	blood
10	chr6:27729200-27730800	Active TSS	Primary T cells from cord blood	blood
11	chr6:27729200-27731000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:27729400-27730200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr6:27729400-27730400	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:27729400-27730600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:27729400-27730600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
17	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
19	chr6:27729400-27730600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr6:27729400-27730600	Active TSS	Thymus	Thymus
21	chr6:27729400-27730800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:27729400-27730800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:27729600-27730000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:27729600-27730000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:27729600-27730800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:27729600-27731000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:27729600-27732600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:27729600-27737000	Weak transcription	K562	blood
29	chr6:27729800-27730800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:27729800-27730800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:27729800-27730800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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