Variant report

Variant	rs1016146
Chromosome Location	chr6:35445516-35445517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35421073..35422894-chr6:35443794..35445610,2	K562	blood:
2	chr6:35259275..35263852-chr6:35441869..35446640,5	K562	blood:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11962335	1.00[YRI][hapmap]
rs12204518	0.81[EUR][1000 genomes]
rs2076173	1.00[YRI][hapmap]
rs2894401	0.81[MEX][hapmap]
rs3800377	0.84[ASW][hapmap];0.80[CEU][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4713864	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4713867	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4713868	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs760782	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7757405	0.92[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
2	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
5	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1016146	RPL10A	cis	cerebellum	SCAN
rs1016146	FGD2	cis	cerebellum	SCAN
rs1016146	PPIL1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35437600-35449200	Strong transcription	Aorta	Aorta
2	chr6:35437800-35446200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:35437800-35451000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:35438000-35455800	Weak transcription	Brain Angular Gyrus	brain
5	chr6:35438200-35458000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:35438400-35449600	Strong transcription	Gastric	stomach
7	chr6:35438800-35448200	Strong transcription	Right Ventricle	heart
8	chr6:35439200-35447600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:35439200-35447600	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:35439200-35447800	Strong transcription	Colonic Mucosa	Colon
11	chr6:35439200-35448200	Strong transcription	Lung	lung
12	chr6:35439200-35452400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:35439200-35452600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:35439200-35453000	Weak transcription	Fetal Kidney	kidney
15	chr6:35439400-35452600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr6:35439800-35452600	Strong transcription	Fetal Intestine Small	intestine
17	chr6:35440000-35452400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:35440200-35447400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:35440200-35447600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr6:35440200-35448200	Strong transcription	Ovary	ovary
21	chr6:35440200-35452200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:35440200-35452400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:35440200-35457200	Weak transcription	Psoas Muscle	Psoas
24	chr6:35440400-35446600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:35440400-35449400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:35440400-35452400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:35440400-35452400	Weak transcription	Hela-S3	cervix
28	chr6:35440400-35452600	Strong transcription	NHLF	lung
29	chr6:35440400-35452800	Strong transcription	Fetal Stomach	stomach
30	chr6:35440400-35453000	Strong transcription	Fetal Intestine Large	intestine
31	chr6:35440400-35455600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:35440600-35445600	Weak transcription	Dnd41	blood
33	chr6:35440600-35446800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:35440600-35448600	Strong transcription	Liver	Liver
35	chr6:35440600-35455800	Weak transcription	Primary B cells from cord blood	blood
36	chr6:35440800-35452600	Weak transcription	NHDF-Ad	bronchial
37	chr6:35441200-35446000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:35441200-35446400	Strong transcription	Pancreas	Pancrea
39	chr6:35441200-35448200	Weak transcription	K562	blood
40	chr6:35441200-35452600	Weak transcription	A549	lung
41	chr6:35441400-35446000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:35441400-35447800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:35441400-35450200	Strong transcription	Colon Smooth Muscle	Colon
44	chr6:35441400-35452200	Weak transcription	HSMM	muscle
45	chr6:35441400-35452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:35441400-35452400	Weak transcription	HMEC	breast
47	chr6:35441400-35452800	Weak transcription	HUVEC	blood vessel
48	chr6:35441800-35447200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:35441800-35447400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:35441800-35448200	Strong transcription	Left Ventricle	heart

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