Variant report

Variant	rs3129973
Chromosome Location	chr6:30721143-30721144
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	chr6:30718958..30721409-chr6:30812435..30814738,2	MCF-7	breast:
2	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
3	chr6:30719980..30722525-chr6:30838687..30841079,2	K562	blood:
4	chr6:30718989..30721292-chr6:30772340..30774126,2	MCF-7	breast:
5	chr6:30717879..30721732-chr6:30850020..30854415,6	MCF-7	breast:
6	chr6:30719096..30721371-chr6:30880176..30882987,2	MCF-7	breast:
7	chr6:30582929..30584442-chr6:30719017..30721240,2	MCF-7	breast:
8	chr6:30720410..30722435-chr6:30765919..30768598,2	MCF-7	breast:
9	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
10	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237775	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1049633	0.81[AMR][1000 genomes]
rs1059612	0.91[AMR][1000 genomes];0.89[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];0.86[EUR][1000 genomes]
rs1264361	0.82[EUR][1000 genomes]
rs1264373	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2263298	0.81[AMR][1000 genomes]
rs2517578	0.81[AMR][1000 genomes]
rs2524266	0.86[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	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3094125	0.87[EUR][1000 genomes]
rs3095276	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095327	0.81[EUR][1000 genomes]
rs3095328	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095332	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095334	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129972	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3129974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129977	0.91[EUR][1000 genomes]
rs3129978	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129980	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129982	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129983	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129984	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3129985	0.84[AMR][1000 genomes];0.83[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];0.86[EUR][1000 genomes]
rs3130658	0.87[EUR][1000 genomes]
rs3130660	0.87[EUR][1000 genomes]
rs3130665	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130668	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130669	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130670	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130673	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131041	0.88[EUR][1000 genomes]
rs3131044	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131045	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131047	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131049	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131050	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131052	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3131055	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131058	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131060	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3132577	0.81[AMR][1000 genomes]
rs3132582	0.81[EUR][1000 genomes]
rs3132583	0.87[EUR][1000 genomes]
rs3132585	0.87[EUR][1000 genomes]
rs3132599	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3132603	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132605	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132610	0.82[AMR][1000 genomes]
rs886422	0.81[AMR][1000 genomes]
rs886424	0.82[EUR][1000 genomes]
rs886425	0.82[EUR][1000 genomes]
rs9262126	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262130	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262132	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262135	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262141	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262142	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262143	0.83[EUR][1000 genomes]
rs9262146	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262200	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262202	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262203	0.84[AMR][1000 genomes]
rs9262204	0.84[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3129973	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3129973	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30712600-30724000	Enhancers	HMEC	breast
2	chr6:30714200-30721200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:30715200-30722200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:30715600-30721600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:30716600-30721400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr6:30717000-30724000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:30717200-30721400	Enhancers	HUVEC	blood vessel
8	chr6:30717800-30721200	Enhancers	Stomach Mucosa	stomach
9	chr6:30717800-30725400	Weak transcription	Spleen	Spleen
10	chr6:30717800-30726800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:30718600-30723600	Weak transcription	Liver	Liver
12	chr6:30719000-30721200	Enhancers	Fetal Muscle Leg	muscle
13	chr6:30719200-30721200	Enhancers	Adipose Nuclei	Adipose
14	chr6:30719200-30721200	Enhancers	Placenta	Placenta
15	chr6:30719200-30721200	Enhancers	Left Ventricle	heart
16	chr6:30719200-30721400	Enhancers	Fetal Heart	heart
17	chr6:30719200-30721600	Enhancers	Colon Smooth Muscle	Colon
18	chr6:30719400-30721200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:30719400-30721200	Enhancers	Psoas Muscle	Psoas
20	chr6:30719400-30721200	Enhancers	Right Ventricle	heart
21	chr6:30719400-30721400	Enhancers	Fetal Stomach	stomach
22	chr6:30719600-30721200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:30719600-30721200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:30719600-30725000	Weak transcription	GM12878-XiMat	blood
25	chr6:30719800-30721200	Enhancers	Brain Hippocampus Middle	brain
26	chr6:30719800-30721200	Enhancers	Small Intestine	intestine
27	chr6:30719800-30721400	Enhancers	Rectal Smooth Muscle	rectum
28	chr6:30719800-30723200	Enhancers	HSMM	muscle
29	chr6:30719800-30727200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:30719800-30731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:30720000-30721200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:30720000-30721400	Enhancers	NHLF	lung
33	chr6:30720000-30721600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:30720000-30723200	Enhancers	HSMMtube	muscle
35	chr6:30720000-30724000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:30720000-30724000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:30720000-30724000	Enhancers	NHDF-Ad	bronchial
38	chr6:30720000-30724000	Enhancers	Osteobl	bone
39	chr6:30720000-30725800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:30720200-30721200	Enhancers	Right Atrium	heart
41	chr6:30720200-30721400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:30720200-30721400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr6:30720200-30723000	Enhancers	A549	lung
44	chr6:30720200-30723000	Enhancers	NH-A	brain
45	chr6:30720400-30721200	Enhancers	Colonic Mucosa	Colon
46	chr6:30720400-30725800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:30720400-30731000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:30720600-30721400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:30720600-30723200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:30720600-30723800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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