Variant report

Variant	rs11757306
Chromosome Location	chr6:30807058-30807059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30806333..30810243-chr6:30843203..30846067,3	K562	blood:
2	chr6:30807011..30808968-chr6:30850726..30853143,2	MCF-7	breast:
3	chr6:30807003..30808509-chr6:30812271..30813825,2	K562	blood:
4	chr6:30805834..30810192-chr6:30850275..30853725,4	MCF-7	breast:
5	chr6:30806007..30809728-chr6:30842937..30845561,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-12	chr6:30805173-30807796	NONHSAT108684

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000237775	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11757361	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11758183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264350	0.86[ASN][1000 genomes]
rs28744105	0.86[ASN][1000 genomes]
rs55745908	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57065637	0.86[ASN][1000 genomes]
rs57817411	0.86[ASN][1000 genomes]
rs58554612	0.86[ASN][1000 genomes]
rs58594197	0.86[ASN][1000 genomes]
rs6457281	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73425726	0.86[ASN][1000 genomes]
rs73432796	0.86[ASN][1000 genomes]
rs73432800	0.86[ASN][1000 genomes]
rs73434604	0.86[ASN][1000 genomes]
rs73434608	0.86[ASN][1000 genomes]
rs73437885	0.86[ASN][1000 genomes]
rs73727119	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73727120	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73727123	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7746003	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv526110	chr6:30800577-30810654	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11757306	HCG27	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30796800-30811000	Weak transcription	Right Ventricle	heart
2	chr6:30797000-30808400	Weak transcription	Esophagus	oesophagus
3	chr6:30797200-30812000	Weak transcription	Lung	lung
4	chr6:30798400-30809000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:30799200-30812200	Weak transcription	Spleen	Spleen
6	chr6:30800600-30807400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:30803000-30807400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:30803200-30808200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:30803200-30808600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:30803200-30808800	Weak transcription	Primary T cells from cord blood	blood
11	chr6:30803200-30809200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:30803200-30809200	Weak transcription	Right Atrium	heart
13	chr6:30803200-30811400	Enhancers	Fetal Thymus	thymus
14	chr6:30803200-30811400	Enhancers	Thymus	Thymus
15	chr6:30803400-30808200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:30803400-30808800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:30803400-30809400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:30803600-30808400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:30803600-30808800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:30803800-30811200	Enhancers	Dnd41	blood
21	chr6:30804400-30807600	Weak transcription	HMEC	breast
22	chr6:30804600-30809800	Weak transcription	Fetal Kidney	kidney
23	chr6:30804600-30811200	Weak transcription	Adipose Nuclei	Adipose
24	chr6:30804600-30811200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:30804600-30811600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:30804800-30809000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:30805000-30809000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:30805000-30809200	Weak transcription	Left Ventricle	heart
29	chr6:30805000-30809200	Weak transcription	Osteobl	bone
30	chr6:30805000-30809400	Weak transcription	HSMMtube	muscle
31	chr6:30805000-30811000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:30805200-30809000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:30805400-30807600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:30805600-30807800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr6:30805600-30809400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:30805600-30811200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:30805800-30807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:30805800-30808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:30805800-30809800	Weak transcription	Fetal Heart	heart
40	chr6:30805800-30811000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:30805800-30811200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:30806000-30807600	Weak transcription	A549	lung
43	chr6:30806000-30807600	Weak transcription	K562	blood
44	chr6:30806000-30809200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:30806000-30809800	Weak transcription	Fetal Lung	lung
46	chr6:30806400-30808200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:30806400-30810000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:30806600-30807400	Enhancers	Hela-S3	cervix
49	chr6:30806600-30807800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:30806600-30808400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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