Variant report

Variant	rs2517462
Chromosome Location	chr6:30896190-30896191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30882885..30885102-chr6:30895534..30897126,2	MCF-7	breast:
2	chr6:30840919..30843118-chr6:30894417..30896304,2	K562	blood:
3	chr6:30895904..30897988-chr6:30898717..30900643,2	MCF-7	breast:
4	chr6:30693361..30695767-chr6:30895208..30897558,2	K562	blood:

Variant related genes	Relation type
ENSG00000252761	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000196260	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264342	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189763	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2074506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240804	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517449	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2517461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517463	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517573	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517575	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517577	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517582	0.86[EUR][1000 genomes]
rs2532920	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2532921	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2532927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2532928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2532929	0.90[EUR][1000 genomes]
rs2532930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2532933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2532936	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535325	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535326	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2535327	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535329	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535330	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535335	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535336	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535337	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844655	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844658	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844662	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844663	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844664	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844698	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844699	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844702	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130657	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7738138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs887381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9262288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262291	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2517462	HCG22	cis	lymphoblastoid	seeQTL
rs2517462	GRM4	cis	parietal	SCAN
rs2517462	HIST1H2BL	cis	parietal	SCAN
rs2517462	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs2517462	VARS2	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30883400-30897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:30883800-30896600	Strong transcription	Fetal Muscle Leg	muscle
3	chr6:30884000-30896200	Strong transcription	Fetal Thymus	thymus
4	chr6:30884000-30897000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:30884200-30896200	Strong transcription	Fetal Brain Female	brain
6	chr6:30884600-30896200	Strong transcription	Liver	Liver
7	chr6:30884800-30896400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:30884800-30896600	Strong transcription	Brain Germinal Matrix	brain
9	chr6:30885000-30896600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:30885600-30896200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:30887200-30896600	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr6:30889400-30900000	Weak transcription	Small Intestine	intestine
13	chr6:30890800-30896200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:30891600-30896400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:30891800-30896200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:30892600-30899600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:30893400-30896600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:30894000-30896400	Strong transcription	Primary B cells from cord blood	blood
19	chr6:30894200-30896600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:30894200-30898800	Weak transcription	NHLF	lung
21	chr6:30894400-30896200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:30894400-30896200	Weak transcription	Osteobl	bone
23	chr6:30894400-30896400	Weak transcription	Brain Substantia Nigra	brain
24	chr6:30894400-30896400	Weak transcription	NH-A	brain
25	chr6:30894600-30896200	Weak transcription	Esophagus	oesophagus
26	chr6:30894600-30896400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:30894600-30896400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:30894600-30896400	Weak transcription	A549	lung
29	chr6:30894600-30896800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:30894800-30896200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:30894800-30896200	Weak transcription	Adipose Nuclei	Adipose
32	chr6:30894800-30896200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:30894800-30896200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:30894800-30896200	Weak transcription	HSMM	muscle
35	chr6:30894800-30896400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:30894800-30896400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:30894800-30896400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:30894800-30896400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:30894800-30896400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:30894800-30896400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:30894800-30896400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:30894800-30896400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:30894800-30896400	Weak transcription	Brain Angular Gyrus	brain
44	chr6:30894800-30896400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:30894800-30896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:30894800-30896400	Weak transcription	Spleen	Spleen
47	chr6:30894800-30896400	Weak transcription	HepG2	liver
48	chr6:30894800-30896600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:30894800-30896600	Weak transcription	Left Ventricle	heart
50	chr6:30894800-30896600	Weak transcription	Pancreas	Pancrea

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