Variant report

Variant	rs9262130
Chromosome Location	chr6:30603519-30603520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30603404..30605348-chr6:30605560..30609450,3	MCF-7	breast:
2	chr6:30601918..30605372-chr6:30687012..30690435,4	K562	blood:
3	chr6:30592203..30595028-chr6:30602897..30604567,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137343	Chromatin interaction
ENSG00000196230	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264351	1.00[AMR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs2524266	0.83[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3094118	0.83[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3095327	0.88[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3095334	0.82[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129977	0.80[EUR][1000 genomes]
rs3129978	0.82[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130665	0.83[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes]
rs3130673	0.82[EUR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3132582	0.88[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132599	0.82[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3132603	0.82[EUR][1000 genomes]
rs3132605	0.82[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262143	0.97[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[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	nsv969376	chr6:30601427-30608408	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9262130	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30593600-30613800	Weak transcription	Hela-S3	cervix
2	chr6:30595200-30607000	Weak transcription	Right Atrium	heart
3	chr6:30595200-30609000	Weak transcription	Colonic Mucosa	Colon
4	chr6:30595400-30607800	Weak transcription	Right Ventricle	heart
5	chr6:30595400-30608200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:30595400-30608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:30595400-30614000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:30595400-30614800	Weak transcription	Small Intestine	intestine
9	chr6:30595600-30605200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:30595600-30608000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:30595600-30608200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:30595600-30608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:30595600-30611000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:30595600-30613000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:30595600-30613800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:30595600-30614200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:30595600-30614200	Strong transcription	Fetal Stomach	stomach
18	chr6:30595600-30614200	Weak transcription	Psoas Muscle	Psoas
19	chr6:30595600-30614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:30595800-30604200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:30595800-30608200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:30595800-30608800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:30595800-30613000	Strong transcription	Fetal Lung	lung
24	chr6:30595800-30613600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:30595800-30613600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:30595800-30614000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:30595800-30614200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:30596000-30604200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:30596000-30605200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:30596000-30605400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:30596000-30605800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:30596000-30613800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:30596000-30613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:30596000-30614000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:30596000-30614000	Strong transcription	Fetal Muscle Leg	muscle
36	chr6:30596000-30614200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:30596200-30606600	Strong transcription	Brain Germinal Matrix	brain
38	chr6:30596200-30610600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:30596200-30611600	Strong transcription	Fetal Intestine Small	intestine
40	chr6:30596200-30612600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:30596200-30613600	Weak transcription	Fetal Heart	heart
42	chr6:30596200-30613600	Weak transcription	HUVEC	blood vessel
43	chr6:30596200-30614200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:30596200-30614200	Strong transcription	Fetal Brain Female	brain
45	chr6:30597000-30608000	Weak transcription	Fetal Brain Male	brain
46	chr6:30597800-30608200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr6:30598000-30607600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:30598000-30607600	Weak transcription	Fetal Kidney	kidney
49	chr6:30598000-30608000	Weak transcription	GM12878-XiMat	blood
50	chr6:30598800-30608200	Weak transcription	Muscle Satellite Cultured Cells	--

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