Variant report

Variant	rs9262142
Chromosome Location	chr6:30650026-30650027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30649121..30651445-chr6:30738828..30742388,3	K562	blood:
2	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
3	chr6:30648844..30650504-chr6:30769704..30772365,2	K562	blood:
4	chr6:30649806..30652040-chr6:30852891..30855625,2	MCF-7	breast:
5	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
6	chr6:30648527..30651008-chr6:30780942..30782992,2	K562	blood:
7	chr6:30581835..30584351-chr6:30648631..30650340,3	MCF-7	breast:
8	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
9	chr6:30648195..30650170-chr6:30674110..30676908,2	MCF-7	breast:
10	chr6:30648927..30651629-chr6:30742930..30745365,2	K562	blood:
11	chr6:30642982..30645092-chr6:30648552..30650727,2	MCF-7	breast:
12	chr6:30649925..30651436-chr6:30850377..30852491,2	MCF-7	breast:
13	chr6:30537901..30539493-chr6:30647818..30650162,2	K562	blood:
14	chr6:30640371..30641343-chr6:30649995..30650632,2	K562	blood:
15	chr6:30643814..30650234-chr6:30705979..30710789,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196230	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1264347	0.90[AMR][1000 genomes]
rs1264351	1.00[AMR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs2263298	0.90[AMR][1000 genomes]
rs2517578	0.90[AMR][1000 genomes]
rs2524266	0.83[AMR][1000 genomes]
rs2535328	0.90[AMR][1000 genomes]
rs2535332	0.90[AMR][1000 genomes]
rs2535334	0.90[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3094118	0.80[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3095327	0.85[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130665	0.80[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3132582	0.85[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262143	1.00[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv884095	chr6:30644987-30664567	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884096	chr6:30647979-30664567	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9262142	HIST1H2BM	cis	cerebellum	SCAN
rs9262142	ZNF323	cis	parietal	SCAN
rs9262142	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs9262142	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30644200-30653800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:30645000-30651800	Weak transcription	Ovary	ovary
3	chr6:30645400-30650200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:30646600-30650600	Enhancers	Fetal Brain Male	brain
5	chr6:30646600-30653400	Transcr. at gene 5' and 3'	NHLF	lung
6	chr6:30646600-30653800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:30646800-30650200	Weak transcription	Fetal Kidney	kidney
8	chr6:30646800-30650600	Genic enhancers	Spleen	Spleen
9	chr6:30646800-30651200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
10	chr6:30646800-30653200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:30646800-30653600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:30646800-30653800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:30647000-30650200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30647000-30651600	Transcr. at gene 5' and 3'	Osteobl	bone
15	chr6:30647000-30653400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
16	chr6:30647000-30653800	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr6:30647200-30650200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:30647400-30653600	Transcr. at gene 5' and 3'	NHEK	skin
19	chr6:30647600-30650600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:30648000-30650200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:30648000-30650600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:30648200-30650400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr6:30648200-30651400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr6:30648400-30650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:30648400-30650600	Weak transcription	Brain Angular Gyrus	brain
26	chr6:30648400-30654400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:30648600-30650400	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:30648600-30655600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:30648800-30650400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr6:30648800-30651000	Transcr. at gene 5' and 3'	HSMM	muscle
31	chr6:30648800-30651400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
32	chr6:30648800-30651600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:30649000-30650400	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:30649000-30650400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:30649000-30651200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr6:30649000-30653800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
37	chr6:30649000-30656200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:30649200-30650200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:30649200-30650200	Active TSS	NHDF-Ad	bronchial
40	chr6:30649200-30650400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr6:30649200-30650400	Flanking Active TSS	Thymus	Thymus
42	chr6:30649200-30650400	Flanking Active TSS	HUVEC	blood vessel
43	chr6:30649200-30650600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr6:30649200-30650800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:30649200-30651000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:30649200-30652200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr6:30649200-30652800	Active TSS	HSMMtube	muscle
48	chr6:30649200-30654000	Active TSS	Brain Hippocampus Middle	brain
49	chr6:30649200-30654400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr6:30649200-30655200	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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