Variant report

Variant	rs3095276
Chromosome Location	chr6:30566407-30566408
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30565006..30567611-chr6:30709918..30712525,2	K562	blood:
2	chr6:30463933..30465752-chr6:30565094..30566698,2	MCF-7	breast:
3	chr6:30537577..30540072-chr6:30565353..30567692,2	MCF-7	breast:
4	chr6:30566253..30568744-chr6:30622206..30624656,2	K562	blood:
5	chr6:30565122..30567230-chr6:30697537..30699633,2	MCF-7	breast:
6	chr6:30464414..30466263-chr6:30565221..30566781,2	K562	blood:
7	chr6:30507925..30510897-chr6:30565235..30566858,2	MCF-7	breast:
8	chr6:30449909..30452819-chr6:30563358..30566713,3	K562	blood:
9	chr6:30449909..30451600-chr6:30563747..30566713,2	K562	blood:
10	chr6:30563905..30566621-chr6:30688616..30691051,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204574	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3094717	0.80[AMR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.84[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]
rs3132583	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132619	0.80[AMR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262143	0.92[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[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	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases
8	nsv5244	chr6:30545111-30589803	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	772 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3095276	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:30541400-30567400	Weak transcription	Fetal Heart	heart
4	chr6:30542200-30581800	Weak transcription	Right Atrium	heart
5	chr6:30554800-30569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:30558000-30568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:30558800-30568400	Weak transcription	Esophagus	oesophagus
8	chr6:30558800-30569200	Weak transcription	Fetal Brain Male	brain
9	chr6:30559000-30568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:30559000-30568800	Weak transcription	Small Intestine	intestine
11	chr6:30559200-30568400	Weak transcription	Right Ventricle	heart
12	chr6:30559200-30568800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:30559200-30568800	Weak transcription	Stomach Mucosa	stomach
14	chr6:30559200-30569000	Weak transcription	Brain Angular Gyrus	brain
15	chr6:30559200-30569000	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:30559600-30568400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:30560200-30568400	Weak transcription	Gastric	stomach
18	chr6:30560400-30568200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:30560400-30568400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:30560400-30568400	Weak transcription	NHDF-Ad	bronchial
21	chr6:30560400-30569400	Weak transcription	Psoas Muscle	Psoas
22	chr6:30560600-30566600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:30560600-30568200	Weak transcription	A549	lung
24	chr6:30560600-30568400	Weak transcription	Brain Substantia Nigra	brain
25	chr6:30560600-30568400	Weak transcription	Colonic Mucosa	Colon
26	chr6:30560600-30568400	Weak transcription	Left Ventricle	heart
27	chr6:30560800-30568400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:30560800-30568400	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:30560800-30568400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:30560800-30568400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:30560800-30569400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:30561200-30567200	Weak transcription	HUVEC	blood vessel
33	chr6:30561200-30568000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:30561400-30567400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:30562600-30568600	Weak transcription	HepG2	liver
36	chr6:30562600-30569200	Weak transcription	Fetal Kidney	kidney
37	chr6:30562800-30566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:30562800-30566800	Weak transcription	Thymus	Thymus
39	chr6:30562800-30567400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:30562800-30568000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:30562800-30568000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:30562800-30568200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:30562800-30568200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:30562800-30568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:30562800-30568400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:30562800-30568400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:30562800-30568400	Weak transcription	Adipose Nuclei	Adipose
48	chr6:30562800-30568400	Weak transcription	Lung	lung
49	chr6:30562800-30568400	Weak transcription	Pancreas	Pancrea
50	chr6:30562800-30568400	Weak transcription	Rectal Smooth Muscle	rectum

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