Variant report

Variant	rs3129974
Chromosome Location	chr6:30723169-30723170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30723023..30725231-chr6:30773189..30775905,2	MCF-7	breast:
2	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
3	chr6:30721626..30724111-chr6:30729705..30731621,2	K562	blood:

Variant related genes	Relation type
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1049633	0.81[AMR][1000 genomes]
rs1059612	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1264308	0.81[AMR][1000 genomes]
rs1264325	0.81[AMR][1000 genomes]
rs1264347	0.81[AMR][1000 genomes]
rs1264351	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264361	0.83[EUR][1000 genomes]
rs1264373	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2263298	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2517578	0.81[AMR][1000 genomes]
rs2524266	0.87[EUR][1000 genomes]
rs2535328	0.81[AMR][1000 genomes]
rs2535332	0.81[AMR][1000 genomes]
rs2535334	0.81[AMR][1000 genomes]
rs2535340	0.81[AMR][1000 genomes]
rs2844656	0.81[AMR][1000 genomes]
rs3094023	0.91[AMR][1000 genomes]
rs3094024	0.81[AMR][1000 genomes]
rs3094088	0.81[AMR][1000 genomes]
rs3094118	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3094125	0.89[EUR][1000 genomes]
rs3095276	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3095326	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095327	0.82[EUR][1000 genomes]
rs3095328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095332	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095334	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129972	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3129973	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129977	0.92[EUR][1000 genomes]
rs3129978	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129980	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129982	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129983	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129984	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129985	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130117	0.91[AMR][1000 genomes]
rs3130241	0.81[AMR][1000 genomes]
rs3130247	0.91[AMR][1000 genomes]
rs3130641	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130658	0.89[EUR][1000 genomes]
rs3130660	0.89[EUR][1000 genomes]
rs3130665	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130668	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130669	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130670	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130673	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131041	0.89[EUR][1000 genomes]
rs3131044	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131045	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131047	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131048	0.81[EUR][1000 genomes]
rs3131049	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131050	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131052	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131055	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131058	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131060	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132577	0.81[AMR][1000 genomes]
rs3132582	0.82[EUR][1000 genomes]
rs3132583	0.89[EUR][1000 genomes]
rs3132585	0.89[EUR][1000 genomes]
rs3132599	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132600	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132603	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132605	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132610	0.82[AMR][1000 genomes]
rs886422	0.81[AMR][1000 genomes]
rs886424	0.83[EUR][1000 genomes]
rs886425	0.83[EUR][1000 genomes]
rs9262126	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262130	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262132	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262135	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262141	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262142	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262143	0.84[EUR][1000 genomes]
rs9262146	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262200	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9262202	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9262203	0.84[AMR][1000 genomes]
rs9262204	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
5	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
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3129974	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30712600-30724000	Enhancers	HMEC	breast
2	chr6:30717000-30724000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:30717800-30725400	Weak transcription	Spleen	Spleen
4	chr6:30717800-30726800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:30718600-30723600	Weak transcription	Liver	Liver
6	chr6:30719600-30725000	Weak transcription	GM12878-XiMat	blood
7	chr6:30719800-30723200	Enhancers	HSMM	muscle
8	chr6:30719800-30727200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:30719800-30731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:30720000-30723200	Enhancers	HSMMtube	muscle
11	chr6:30720000-30724000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:30720000-30724000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:30720000-30724000	Enhancers	NHDF-Ad	bronchial
14	chr6:30720000-30724000	Enhancers	Osteobl	bone
15	chr6:30720000-30725800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:30720400-30725800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:30720400-30731000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:30720600-30723200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:30720600-30723800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:30720600-30736600	Weak transcription	Gastric	stomach
21	chr6:30720800-30724400	Weak transcription	HepG2	liver
22	chr6:30720800-30727000	Weak transcription	Pancreas	Pancrea
23	chr6:30720800-30727600	Weak transcription	Lung	lung
24	chr6:30720800-30727800	Weak transcription	Esophagus	oesophagus
25	chr6:30721000-30723200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:30721000-30725200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:30721000-30725200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:30721000-30725200	Weak transcription	K562	blood
29	chr6:30721000-30725600	Enhancers	NHEK	skin
30	chr6:30721000-30727400	Weak transcription	Aorta	Aorta
31	chr6:30721200-30723600	Weak transcription	Placenta	Placenta
32	chr6:30721200-30723800	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:30721200-30724000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:30721200-30725200	Weak transcription	Right Atrium	heart
35	chr6:30721200-30725200	Weak transcription	Right Ventricle	heart
36	chr6:30721200-30725400	Weak transcription	Left Ventricle	heart
37	chr6:30721200-30725800	Weak transcription	Small Intestine	intestine
38	chr6:30721200-30726400	Weak transcription	Adipose Nuclei	Adipose
39	chr6:30721200-30726800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:30721200-30727000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:30721200-30727600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:30721400-30724800	Weak transcription	Fetal Heart	heart
43	chr6:30721400-30725000	Weak transcription	HUVEC	blood vessel
44	chr6:30721400-30725200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:30721400-30725200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:30721400-30725400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:30721400-30727400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:30721600-30726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:30721800-30724000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:30721800-30726800	Weak transcription	Stomach Smooth Muscle	stomach

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