Variant report

Variant	rs3094088
Chromosome Location	chr6:30894965-30894966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30840919..30843118-chr6:30894417..30896304,2	K562	blood:
2	chr6:30891056..30892872-chr6:30894478..30895984,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1049633	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264351	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1264361	0.87[EUR][1000 genomes]
rs1264373	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1634716	1.00[AMR][1000 genomes]
rs1634721	1.00[AMR][1000 genomes]
rs1634726	0.89[AMR][1000 genomes]
rs2263298	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517546	0.90[AMR][1000 genomes]
rs2517578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2524266	0.92[EUR][1000 genomes]
rs2535328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844661	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095152	0.81[AMR][1000 genomes]
rs3095153	0.81[AMR][1000 genomes]
rs3095156	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes]
rs3129980	0.80[EUR][1000 genomes]
rs3129982	0.80[EUR][1000 genomes]
rs3129983	0.80[EUR][1000 genomes]
rs3129984	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129985	0.80[EUR][1000 genomes]
rs3130574	1.00[AMR][1000 genomes]
rs3130641	0.83[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes]
rs3131041	0.82[EUR][1000 genomes]
rs3131044	0.80[EUR][1000 genomes]
rs3131045	0.80[EUR][1000 genomes]
rs3131047	0.80[EUR][1000 genomes]
rs3131049	0.80[EUR][1000 genomes]
rs3131050	0.80[EUR][1000 genomes]
rs3131052	0.81[EUR][1000 genomes]
rs3131055	0.80[EUR][1000 genomes]
rs3131058	0.80[EUR][1000 genomes]
rs3131060	0.80[EUR][1000 genomes]
rs3131781	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3131920	1.00[AMR][1000 genomes]
rs3132577	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132580	0.81[AMR][1000 genomes]
rs3132581	0.81[AMR][1000 genomes]
rs3132600	0.81[EUR][1000 genomes]
rs886422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886424	0.87[EUR][1000 genomes]
rs886425	0.87[EUR][1000 genomes]
rs9262200	0.80[EUR][1000 genomes]
rs9262202	0.80[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	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	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv884126	chr6:30886350-30895990	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3094088	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30883400-30895800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:30883400-30897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:30883800-30895200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30883800-30895800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:30883800-30896600	Strong transcription	Fetal Muscle Leg	muscle
6	chr6:30884000-30895000	Strong transcription	Placenta	Placenta
7	chr6:30884000-30895800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr6:30884000-30896000	Strong transcription	Fetal Stomach	stomach
9	chr6:30884000-30896200	Strong transcription	Fetal Thymus	thymus
10	chr6:30884000-30897000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:30884200-30895000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:30884200-30895400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr6:30884200-30895600	Strong transcription	Fetal Intestine Small	intestine
14	chr6:30884200-30896200	Strong transcription	Fetal Brain Female	brain
15	chr6:30884400-30895000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:30884400-30895000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:30884400-30895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:30884400-30895800	Strong transcription	Primary T cells from cord blood	blood
19	chr6:30884600-30895000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:30884600-30895200	Strong transcription	Thymus	Thymus
21	chr6:30884600-30895400	Strong transcription	Ovary	ovary
22	chr6:30884600-30896000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:30884600-30896200	Strong transcription	Liver	Liver
24	chr6:30884800-30895000	Strong transcription	Brain Anterior Caudate	brain
25	chr6:30884800-30896000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:30884800-30896400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:30884800-30896600	Strong transcription	Brain Germinal Matrix	brain
28	chr6:30885000-30895600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:30885000-30896600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:30885600-30896200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:30885800-30895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:30886800-30895000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr6:30887200-30896600	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr6:30887400-30895400	Strong transcription	Brain Hippocampus Middle	brain
35	chr6:30889400-30895200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:30889400-30895400	Weak transcription	HUVEC	blood vessel
37	chr6:30889400-30900000	Weak transcription	Small Intestine	intestine
38	chr6:30889600-30896000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:30890400-30895800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:30890800-30896200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:30891400-30896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:30891600-30895000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:30891600-30896400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:30891800-30896200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:30892600-30899600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:30893200-30895200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:30893400-30895000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:30893400-30895200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:30893400-30896600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:30893800-30895000	Strong transcription	Primary hematopoietic stem cells	blood

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