Variant report

Variant	rs3130932
Chromosome Location	chr6:31133943-31133944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31129733..31135466-chr6:31137398..31140077,6	K562	blood:
2	chr6:31130035..31132882-chr6:31132970..31134557,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204531	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1061118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1065461	0.82[ASN][1000 genomes]
rs2073721	0.82[ASN][1000 genomes]
rs2073723	0.82[ASN][1000 genomes]
rs2106074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240059	0.82[ASN][1000 genomes]
rs2394882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094192	0.83[ASN][1000 genomes]
rs3130450	0.80[ASN][1000 genomes]
rs3130501	0.84[ASN][1000 genomes]
rs3130502	0.84[ASN][1000 genomes]
rs3130504	0.83[ASN][1000 genomes]
rs3130928	0.80[ASN][1000 genomes]
rs3130929	0.84[ASN][1000 genomes]
rs3130934	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132522	0.83[ASN][1000 genomes]
rs3132523	0.84[ASN][1000 genomes]
rs3132524	0.84[ASN][1000 genomes]
rs3132526	0.80[ASN][1000 genomes]
rs3132528	0.82[ASN][1000 genomes]
rs9263804	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
13	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
14	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv1034391	chr6:31131121-31279595	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
17	nsv1025909	chr6:31131121-31354706	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
18	nsv538175	chr6:31131121-31354706	Active TSS Bivalent Enhancer Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
19	nsv1015890	chr6:31131121-31449207	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
20	nsv538176	chr6:31131121-31449207	Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3130932	HLA-C	cis	lymphoblastoid	GTEx
rs3130932	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3130932	CCHCR1	cis	lymphoblastoid	seeQTL
rs3130932	TCF19	cis	lymphoblastoid	seeQTL
rs3130932	ANKS1A	cis	cerebellum	SCAN
rs3130932	HIST1H3J	cis	parietal	SCAN
rs3130932	ZNF187	cis	cerebellum	SCAN
rs3130932	CCHCR1	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31127200-31140600	Weak transcription	Left Ventricle	heart
2	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
3	chr6:31127600-31136600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:31127600-31137000	Weak transcription	Stomach Mucosa	stomach
5	chr6:31127600-31143000	Weak transcription	Right Ventricle	heart
6	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:31127600-31148000	Weak transcription	Right Atrium	heart
8	chr6:31127800-31136400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:31127800-31136400	Weak transcription	Primary T cells from cord blood	blood
10	chr6:31127800-31142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:31127800-31142800	Weak transcription	HSMM	muscle
12	chr6:31127800-31146200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:31127800-31147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:31127800-31147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:31127800-31153200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:31128000-31135600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:31128000-31136800	Weak transcription	K562	blood
18	chr6:31128000-31137400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:31128000-31140400	Weak transcription	Brain Germinal Matrix	brain
20	chr6:31128000-31143200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:31128200-31135800	Weak transcription	Fetal Brain Female	brain
22	chr6:31128200-31143600	Weak transcription	NHDF-Ad	bronchial
23	chr6:31129200-31134000	Strong transcription	Fetal Stomach	stomach
24	chr6:31129400-31134200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:31130200-31134200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:31130200-31146200	Weak transcription	Lung	lung
27	chr6:31130400-31147800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:31130600-31146800	Weak transcription	Colonic Mucosa	Colon
29	chr6:31130800-31134200	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr6:31130800-31134400	Weak transcription	Ovary	ovary
31	chr6:31130800-31137400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:31130800-31141800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:31131000-31136200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:31131000-31141000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:31131000-31143200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:31131000-31143400	Weak transcription	Esophagus	oesophagus
37	chr6:31131000-31147800	Weak transcription	Adipose Nuclei	Adipose
38	chr6:31131000-31148000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:31131000-31148000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr6:31131200-31136400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:31131200-31143600	Weak transcription	Osteobl	bone
42	chr6:31131400-31134200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:31131400-31134200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:31131400-31136400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:31131400-31142800	Weak transcription	HepG2	liver
46	chr6:31131600-31136800	Weak transcription	NHEK	skin
47	chr6:31131600-31143400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:31131600-31143400	Weak transcription	Fetal Lung	lung
49	chr6:31131600-31143600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:31131800-31138200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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