Variant report

Variant	rs9262135
Chromosome Location	chr6:30618906-30618907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30618886-30618960	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30618619-30619767	K562	blood:	n/a	n/a
3	POLR2A	chr6:30618623-30620112	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:30618648-30619138	K562	blood:	n/a	n/a
5	POLR2A	chr6:30618776-30619168	K562	blood:	n/a	n/a
6	POLR2A	chr6:30618710-30619137	HepG2	liver:	n/a	n/a
7	NFATC1	chr6:30618665-30619315	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:30618671-30619438	K562	blood:	n/a	n/a
9	POLR2A	chr6:30618604-30619254	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:30618697-30619277	K562	blood:	n/a	n/a
11	POLR2A	chr6:30618694-30619049	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr6:30618687-30618978	HCT-116	colon:	n/a	n/a
13	MTA3	chr6:30618897-30619323	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:30618584-30619623	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr6:30618737-30619138	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr6:30618288-30619087	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:30618628-30619174	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr6:30618673-30619409	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30580789..30587552-chr6:30608606..30620072,66	K562	blood:
2	chr6:30618609..30620115-chr6:30628547..30631052,2	MCF-7	breast:
3	chr6:30609523..30619025-chr6:30620991..30630753,19	MCF-7	breast:
4	chr6:30591157..30598732-chr6:30607879..30619621,21	K562	blood:

No data

Variant related genes	Relation type
C6orf136	TF binding region
ENSG00000204568	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1059612	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264351	0.90[AMR][1000 genomes]
rs1264373	0.90[AMR][1000 genomes]
rs3094023	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3094024	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3094118	0.83[EUR][1000 genomes]
rs3094125	0.95[EUR][1000 genomes]
rs3095276	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3095327	0.88[EUR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3095334	0.82[EUR][1000 genomes]
rs3129972	0.89[EUR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129977	0.80[EUR][1000 genomes]
rs3129978	0.82[EUR][1000 genomes]
rs3129984	0.81[AMR][1000 genomes]
rs3130117	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130241	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130247	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130658	0.95[EUR][1000 genomes]
rs3130660	0.95[EUR][1000 genomes]
rs3130665	0.83[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes]
rs3130673	0.82[EUR][1000 genomes]
rs3132582	0.88[EUR][1000 genomes]
rs3132583	0.95[EUR][1000 genomes]
rs3132585	0.95[EUR][1000 genomes]
rs3132599	0.82[EUR][1000 genomes]
rs3132600	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3132603	0.82[EUR][1000 genomes]
rs3132605	0.82[EUR][1000 genomes]
rs3132610	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262130	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262132	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262141	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262142	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262143	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262146	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
8	nsv884093	chr6:30604955-30618906	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9262135	HIST1H2BM	cis	cerebellum	SCAN
rs9262135	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs9262135	ZNF323	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30615800-30619000	Weak transcription	Aorta	Aorta
2	chr6:30615800-30619000	Weak transcription	Spleen	Spleen
3	chr6:30615800-30619600	Weak transcription	Esophagus	oesophagus
4	chr6:30616000-30627000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:30616200-30619000	Weak transcription	Stomach Mucosa	stomach
6	chr6:30616200-30619400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:30616200-30619400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:30616200-30619800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:30616200-30620200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:30616200-30620200	Weak transcription	HSMM	muscle
11	chr6:30616200-30620200	Weak transcription	NHLF	lung
12	chr6:30616200-30620600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:30616200-30620600	Weak transcription	GM12878-XiMat	blood
14	chr6:30616200-30621000	Weak transcription	HUVEC	blood vessel
15	chr6:30616200-30622000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:30616200-30622400	Weak transcription	NHDF-Ad	bronchial
17	chr6:30616200-30627600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:30616200-30627600	Weak transcription	Fetal Brain Male	brain
19	chr6:30616200-30630800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:30616200-30639800	Weak transcription	Right Atrium	heart
21	chr6:30616400-30619600	Weak transcription	Fetal Lung	lung
22	chr6:30616400-30620200	Weak transcription	Hela-S3	cervix
23	chr6:30616400-30620600	Weak transcription	Fetal Kidney	kidney
24	chr6:30616400-30622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:30617000-30620200	Weak transcription	Fetal Heart	heart
26	chr6:30617200-30621000	Strong transcription	A549	lung
27	chr6:30617200-30628400	Strong transcription	Primary hematopoietic stem cells	blood
28	chr6:30617200-30636200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:30617200-30636400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:30617200-30636600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:30617200-30638600	Strong transcription	Fetal Stomach	stomach
32	chr6:30617200-30638600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:30617200-30638800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:30617200-30638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:30617200-30639000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:30617200-30639000	Strong transcription	Fetal Intestine Small	intestine
37	chr6:30617200-30639000	Strong transcription	Thymus	Thymus
38	chr6:30617400-30623000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:30617400-30623400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:30617400-30630800	Strong transcription	Right Ventricle	heart
41	chr6:30617400-30634200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:30617400-30636000	Strong transcription	Colon Smooth Muscle	Colon
43	chr6:30617400-30636400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:30617400-30636600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr6:30617400-30638400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:30617400-30638600	Strong transcription	Fetal Thymus	thymus
47	chr6:30617400-30638800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:30617400-30639000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr6:30617400-30639000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr6:30617400-30639200	Strong transcription	Fetal Muscle Leg	muscle

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