Variant report

Variant	rs9262132
Chromosome Location	chr6:30611350-30611351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30611005-30611570	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30610971-30611726	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:30611293-30611386	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30583125..30584769-chr6:30610108..30612835,2	MCF-7	breast:
2	chr6:30598934..30603301-chr6:30608761..30613584,7	MCF-7	breast:
3	chr6:30580789..30587552-chr6:30608606..30620072,66	K562	blood:
4	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
5	chr6:30609523..30619025-chr6:30620991..30630753,19	MCF-7	breast:
6	chr6:30610587..30612821-chr6:30652736..30654366,2	K562	blood:
7	chr6:30591157..30598732-chr6:30607879..30619621,21	K562	blood:
8	chr6:30571693..30574153-chr6:30610442..30612157,2	K562	blood:

No data

Variant related genes	Relation type
C6orf136	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000228415	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000196230	Chromatin interaction

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

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

rs_ID	r²[population]
rs1059612	0.81[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	0.81[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	0.81[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	0.81[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	0.81[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	0.80[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]
rs9262130	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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262142	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262143	0.97[EUR][1000 genomes]
rs9262146	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	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	nsv884092	chr6:30604955-30617767	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9262132	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	chr6:30595400-30614000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:30595400-30614800	Weak transcription	Small Intestine	intestine
4	chr6:30595600-30613000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:30595600-30613800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:30595600-30614200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr6:30595600-30614200	Strong transcription	Fetal Stomach	stomach
8	chr6:30595600-30614200	Weak transcription	Psoas Muscle	Psoas
9	chr6:30595600-30614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:30595800-30613000	Strong transcription	Fetal Lung	lung
11	chr6:30595800-30613600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:30595800-30613600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:30595800-30614000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30595800-30614200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:30596000-30613800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:30596000-30613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:30596000-30614000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:30596000-30614000	Strong transcription	Fetal Muscle Leg	muscle
19	chr6:30596000-30614200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:30596200-30611600	Strong transcription	Fetal Intestine Small	intestine
21	chr6:30596200-30612600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:30596200-30613600	Weak transcription	Fetal Heart	heart
23	chr6:30596200-30613600	Weak transcription	HUVEC	blood vessel
24	chr6:30596200-30614200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:30596200-30614200	Strong transcription	Fetal Brain Female	brain
26	chr6:30601400-30614200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:30601800-30613200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:30601800-30613800	Weak transcription	HMEC	breast
29	chr6:30601800-30614000	Weak transcription	Stomach Mucosa	stomach
30	chr6:30601800-30614200	Weak transcription	A549	lung
31	chr6:30602000-30611600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:30602000-30614200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:30603400-30613800	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr6:30603400-30614000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:30603800-30611600	Strong transcription	Fetal Intestine Large	intestine
36	chr6:30606200-30613200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:30606400-30612400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:30606400-30614000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:30606800-30613800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:30606800-30613800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:30607000-30613800	Strong transcription	Brain Hippocampus Middle	brain
42	chr6:30607000-30614000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:30607200-30613600	Strong transcription	Brain Germinal Matrix	brain
44	chr6:30607400-30612600	Strong transcription	Brain Anterior Caudate	brain
45	chr6:30607600-30612000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:30607600-30612000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:30607600-30612200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:30607600-30612600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:30607600-30612600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:30607600-30612600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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