Variant report

Variant	rs3095352
Chromosome Location	chr6:30805921-30805922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30800474..30806072-chr6:30842215..30847924,9	K562	blood:
2	chr6:30803676..30806179-chr6:30849399..30852097,2	MCF-7	breast:
3	chr6:30805834..30810192-chr6:30850275..30853725,4	MCF-7	breast:
4	chr6:30799998..30802555-chr6:30804287..30805987,2	MCF-7	breast:
5	chr6:30793601..30795460-chr6:30804124..30806213,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000237775	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2394449	0.90[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	0.88[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	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095343	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095344	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095346	0.87[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	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095350	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095354	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129990	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129993	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130649	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130650	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130651	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130652	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130653	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130655	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130656	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130786	0.92[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	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130791	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130792	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130793	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130794	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130795	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130796	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131027	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131030	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3131031	0.88[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	0.92[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	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132575	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132576	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132578	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262251	0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3095352	HIST1H2BL	cis	parietal	SCAN

Chromatin state (count:75 , 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	chr6:30798800-30806200	Weak transcription	GM12878-XiMat	blood
6	chr6:30799200-30812200	Weak transcription	Spleen	Spleen
7	chr6:30800600-30807400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:30802800-30806000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:30803000-30807400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:30803200-30806200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:30803200-30808200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:30803200-30808600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:30803200-30808800	Weak transcription	Primary T cells from cord blood	blood
14	chr6:30803200-30809200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:30803200-30809200	Weak transcription	Right Atrium	heart
16	chr6:30803200-30811400	Enhancers	Fetal Thymus	thymus
17	chr6:30803200-30811400	Enhancers	Thymus	Thymus
18	chr6:30803400-30808200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:30803400-30808800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:30803400-30809400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:30803600-30806200	Enhancers	Hela-S3	cervix
22	chr6:30803600-30806400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:30803600-30808400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:30803600-30808800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:30803800-30811200	Enhancers	Dnd41	blood
26	chr6:30804000-30806000	Enhancers	Fetal Lung	lung
27	chr6:30804000-30806800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:30804000-30807000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:30804000-30807000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:30804200-30806600	Enhancers	Brain Germinal Matrix	brain
31	chr6:30804400-30807600	Weak transcription	HMEC	breast
32	chr6:30804600-30809800	Weak transcription	Fetal Kidney	kidney
33	chr6:30804600-30811200	Weak transcription	Adipose Nuclei	Adipose
34	chr6:30804600-30811200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:30804600-30811600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:30804800-30809000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30805000-30806200	Weak transcription	Fetal Stomach	stomach
38	chr6:30805000-30806800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:30805000-30806800	Weak transcription	Placenta	Placenta
40	chr6:30805000-30809000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:30805000-30809200	Weak transcription	Left Ventricle	heart
42	chr6:30805000-30809200	Weak transcription	Osteobl	bone
43	chr6:30805000-30809400	Weak transcription	HSMMtube	muscle
44	chr6:30805000-30811000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:30805200-30807000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr6:30805200-30809000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:30805400-30806400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:30805400-30806800	Enhancers	Primary B cells from cord blood	blood
49	chr6:30805400-30806800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:30805400-30807000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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