Variant report

Variant	rs3130241
Chromosome Location	chr6:30536872-30536873
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	chr6:30482719..30486624-chr6:30535507..30541696,8	K562	blood:
2	chr6:30455992..30459496-chr6:30536691..30539449,3	K562	blood:

Variant related genes	Relation type
ENSG00000235781	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1059612	0.90[AMR][1000 genomes]
rs3094023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095276	0.90[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]
rs3130117	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130247	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes]
rs3131112	0.86[EUR][1000 genomes]
rs3132600	0.90[AMR][1000 genomes]
rs3132610	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132616	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9262126	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262130	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262132	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262135	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262141	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262142	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262143	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262146	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130241	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30526000-30537800	Weak transcription	Small Intestine	intestine
2	chr6:30526000-30538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30526000-30538600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30526200-30538200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:30526400-30538000	Weak transcription	HUVEC	blood vessel
6	chr6:30526400-30538000	Weak transcription	NHDF-Ad	bronchial
7	chr6:30526600-30537800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:30526800-30537600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:30526800-30538200	Weak transcription	Fetal Brain Male	brain
10	chr6:30526800-30538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:30527600-30538000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:30530600-30537600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:30530600-30538200	Weak transcription	Esophagus	oesophagus
14	chr6:30530800-30538000	Weak transcription	Right Ventricle	heart
15	chr6:30531000-30537400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:30531000-30537800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:30531000-30537800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:30531000-30538000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:30531000-30538000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:30531000-30538000	Weak transcription	Aorta	Aorta
21	chr6:30531000-30538000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:30531000-30538000	Weak transcription	HSMMtube	muscle
23	chr6:30531000-30538000	Weak transcription	NHEK	skin
24	chr6:30531000-30538200	Weak transcription	Colonic Mucosa	Colon
25	chr6:30531000-30538200	Weak transcription	Gastric	stomach
26	chr6:30531000-30538400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:30531000-30538400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:30531000-30538600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:30531200-30537800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:30531200-30537800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:30531200-30537800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:30531200-30537800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:30531200-30538000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:30531200-30538000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:30531200-30538000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:30531200-30538000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:30531200-30538200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:30531200-30538200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:30531200-30538200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:30531200-30538200	Weak transcription	HMEC	breast
41	chr6:30531200-30538200	Weak transcription	NH-A	brain
42	chr6:30531200-30538200	Weak transcription	NHLF	lung
43	chr6:30531200-30538400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:30531400-30537800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:30531400-30537800	Enhancers	Liver	Liver
46	chr6:30531400-30537800	Weak transcription	Brain Angular Gyrus	brain
47	chr6:30531400-30537800	Weak transcription	Brain Anterior Caudate	brain
48	chr6:30531400-30537800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:30531400-30537800	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:30531400-30537800	Weak transcription	Fetal Lung	lung

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