Variant report

Variant	rs3130649
Chromosome Location	chr6:30803254-30803255
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30802159-30803617	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:30803122-30803293	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:30802422-30803734	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30707567..30712185-chr6:30801298..30803959,4	MCF-7	breast:
2	chr6:30582933..30584813-chr6:30802694..30804722,2	K562	blood:
3	chr6:30800474..30806072-chr6:30842215..30847924,9	K562	blood:
4	chr6:30796516..30799472-chr6:30801979..30805833,4	MCF-7	breast:
5	chr6:30800305..30802395-chr6:30802717..30804530,3	K562	blood:
6	chr6:30800474..30803474-chr6:30842113..30845625,4	K562	blood:
7	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
8	chr6:30709350..30712510-chr6:30802787..30805110,3	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00243	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs2394449	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2394450	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2394451	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2517582	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2535338	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3094109	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094720	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095342	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095343	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095344	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095346	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095348	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095349	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095350	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095351	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095354	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129990	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129993	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130650	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130651	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130652	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130653	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130655	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130656	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130786	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130787	0.85[EUR][1000 genomes]
rs3130789	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130791	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130792	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130793	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130794	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130795	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130796	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131027	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131030	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3131031	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131033	0.83[ASN][1000 genomes]
rs3131066	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3132573	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3132574	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132575	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132576	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132578	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262251	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130649	VARSL	cis	multi-tissue	Pritchard
rs3130649	HIST1H2BL	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30796200-30805600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:30796200-30805600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:30796400-30805200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:30796400-30805400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:30796800-30804000	Weak transcription	Fetal Heart	heart
6	chr6:30796800-30804000	Weak transcription	Fetal Lung	lung
7	chr6:30796800-30804400	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:30796800-30811000	Weak transcription	Right Ventricle	heart
9	chr6:30797000-30804000	Weak transcription	Adipose Nuclei	Adipose
10	chr6:30797000-30804000	Weak transcription	Left Ventricle	heart
11	chr6:30797000-30808400	Weak transcription	Esophagus	oesophagus
12	chr6:30797200-30804000	Weak transcription	Psoas Muscle	Psoas
13	chr6:30797200-30812000	Weak transcription	Lung	lung
14	chr6:30798000-30805600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:30798000-30805600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:30798000-30805600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:30798400-30804000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:30798400-30804000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:30798400-30809000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:30798800-30804000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:30798800-30805600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:30798800-30806200	Weak transcription	GM12878-XiMat	blood
23	chr6:30799200-30812200	Weak transcription	Spleen	Spleen
24	chr6:30799400-30803400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:30799800-30805600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:30800400-30805000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:30800600-30803600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:30800600-30803600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:30800600-30807400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:30801200-30803400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr6:30801200-30803600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:30801800-30803400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:30802000-30803400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:30802000-30803800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr6:30802200-30803400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:30802200-30803400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr6:30802200-30803400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:30802200-30803800	Flanking Active TSS	Dnd41	blood
39	chr6:30802200-30805000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:30802200-30805000	Enhancers	Osteobl	bone
41	chr6:30802200-30805200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:30802400-30803400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:30802600-30805000	Enhancers	Placenta	Placenta
44	chr6:30802800-30803600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:30802800-30804000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:30802800-30805400	Weak transcription	Primary B cells from cord blood	blood
47	chr6:30802800-30805400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:30802800-30805600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:30802800-30805800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:30802800-30806000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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