Variant report

Variant	rs2517523
Chromosome Location	chr6:31026434-31026435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30883366..30884420-chr6:31026193..31027023,3	MCF-7	breast:
2	chr6:31026121..31026747-chr6:31038216..31039119,3	MCF-7	breast:
3	chr6:31025998..31026666-chr6:31047275..31048136,2	K562	blood:
4	chr6:31025808..31026599-chr6:31047303..31047806,2	MCF-7	breast:
5	chr6:31010860..31013816-chr6:31025922..31027807,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC22-1	chr6:31021984-31027653	XLOC_005243

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1064190	0.81[ASN][1000 genomes]
rs1064191	0.81[ASN][1000 genomes]
rs1265053	0.80[ASN][1000 genomes]
rs1265054	0.81[ASN][1000 genomes]
rs1265055	0.81[ASN][1000 genomes]
rs1265056	0.81[ASN][1000 genomes]
rs1265058	0.81[ASN][1000 genomes]
rs1265059	0.81[ASN][1000 genomes]
rs1265063	0.81[ASN][1000 genomes]
rs1265064	0.81[ASN][1000 genomes]
rs2106067	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2233966	0.80[ASN][1000 genomes]
rs2246330	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249231	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249485	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2249486	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2249876	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2251825	0.85[ASN][1000 genomes]
rs2252195	0.85[ASN][1000 genomes]
rs2256436	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394420	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2394424	0.85[ASN][1000 genomes]
rs2428520	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429721	0.83[ASN][1000 genomes]
rs2517414	0.83[ASN][1000 genomes]
rs2517423	0.83[ASN][1000 genomes]
rs2517427	0.83[ASN][1000 genomes]
rs2517440	0.83[ASN][1000 genomes]
rs2517443	0.80[ASN][1000 genomes]
rs2517450	0.84[ASN][1000 genomes]
rs2517452	0.84[ASN][1000 genomes]
rs2517453	0.84[ASN][1000 genomes]
rs2517455	0.84[ASN][1000 genomes]
rs2517458	0.84[ASN][1000 genomes]
rs2517460	0.84[ASN][1000 genomes]
rs2517464	0.83[ASN][1000 genomes]
rs2517465	0.84[ASN][1000 genomes]
rs2517469	0.80[ASN][1000 genomes]
rs2517470	0.81[ASN][1000 genomes]
rs2517471	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517472	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2517475	0.81[ASN][1000 genomes]
rs2517476	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2517477	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2517478	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2517480	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517483	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2517488	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517489	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517492	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517493	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517497	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517500	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517501	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2517502	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517504	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517507	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517511	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517520	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517524	0.81[AMR][1000 genomes]
rs2517525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517532	0.85[ASN][1000 genomes]
rs2517533	0.85[ASN][1000 genomes]
rs2517534	0.82[ASN][1000 genomes]
rs2517541	0.82[ASN][1000 genomes]
rs2517556	0.81[ASN][1000 genomes]
rs2523836	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2523837	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523838	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523843	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2523846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523854	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523856	0.81[ASN][1000 genomes]
rs2523858	0.85[ASN][1000 genomes]
rs2523860	0.86[ASN][1000 genomes]
rs2523862	0.85[ASN][1000 genomes]
rs2523878	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2523880	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523881	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523883	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2523884	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523885	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523886	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523888	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523889	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523890	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523891	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523893	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523894	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523895	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523896	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535277	0.81[ASN][1000 genomes]
rs2535282	0.83[ASN][1000 genomes]
rs2535283	0.83[ASN][1000 genomes]
rs2535287	0.83[ASN][1000 genomes]
rs2535288	0.83[ASN][1000 genomes]
rs2535289	0.83[ASN][1000 genomes]
rs2535290	0.83[ASN][1000 genomes]
rs2535291	0.83[ASN][1000 genomes]
rs2535292	0.84[ASN][1000 genomes]
rs2535293	0.84[ASN][1000 genomes]
rs2535297	0.84[ASN][1000 genomes]
rs2535299	0.84[ASN][1000 genomes]
rs2535301	0.84[ASN][1000 genomes]
rs2535302	0.82[ASN][1000 genomes]
rs2535303	0.85[ASN][1000 genomes]
rs2535304	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535305	0.86[ASN][1000 genomes]
rs2535306	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2535307	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535308	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535309	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535310	0.86[ASN][1000 genomes]
rs2535311	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2535312	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2535313	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2535314	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2535315	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2844641	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2905757	0.87[ASN][1000 genomes]
rs2905759	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3095305	0.83[ASN][1000 genomes]
rs3130546	0.83[ASN][1000 genomes]
rs3130957	0.83[ASN][1000 genomes]
rs3130959	0.80[ASN][1000 genomes]
rs3130960	0.82[ASN][1000 genomes]
rs3130961	0.84[ASN][1000 genomes]
rs3130962	0.81[ASN][1000 genomes]
rs3130963	0.84[ASN][1000 genomes]
rs3130964	0.84[ASN][1000 genomes]
rs3130970	0.83[ASN][1000 genomes]
rs3131789	0.83[ASN][1000 genomes]
rs3131796	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3915966	0.86[ASN][1000 genomes]
rs6921557	0.82[ASN][1000 genomes]
rs6940894	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6941772	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7381897	0.81[ASN][1000 genomes]
rs7755184	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9262625	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262697	0.84[AMR][1000 genomes]
rs9263456	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9263464	0.82[AMR][1000 genomes]
rs9263465	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9263466	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9263473	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9263474	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9263493	0.84[ASN][1000 genomes]
rs9263494	0.84[ASN][1000 genomes]
rs9263593	0.81[ASN][1000 genomes]
rs9263597	0.82[ASN][1000 genomes]
rs9263631	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv884130	chr6:31014305-31038756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv884131	chr6:31014305-31040725	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv970677	chr6:31020994-31026537	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv884133	chr6:31024673-31036148	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2517523	HCG22	cis	lymphoblastoid	seeQTL
rs2517523	ZNF187	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:31022200-31027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:31022400-31026600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:31022600-31028200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:31022800-31026600	Enhancers	NHEK	skin
7	chr6:31023200-31027600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:31023200-31028200	Enhancers	HMEC	breast
9	chr6:31023800-31027200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:31024200-31026600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:31024400-31027200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:31024600-31026600	Enhancers	HSMMtube	muscle
13	chr6:31024600-31026600	Enhancers	NHDF-Ad	bronchial
14	chr6:31024600-31027600	Enhancers	Brain Substantia Nigra	brain
15	chr6:31024800-31026600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:31024800-31026600	Enhancers	HSMM	muscle
17	chr6:31024800-31026600	Enhancers	NHLF	lung
18	chr6:31024800-31026600	Enhancers	Osteobl	bone
19	chr6:31024800-31027600	Enhancers	Brain Anterior Caudate	brain
20	chr6:31025000-31026600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:31025200-31027400	Enhancers	Brain Hippocampus Middle	brain
22	chr6:31025200-31028200	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:31025400-31026600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:31025400-31027400	Enhancers	Brain Angular Gyrus	brain
25	chr6:31025600-31027400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:31025800-31026600	Enhancers	HUVEC	blood vessel
27	chr6:31026000-31026600	Enhancers	Stomach Mucosa	stomach
28	chr6:31026000-31027200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:31026000-31030200	Weak transcription	Esophagus	oesophagus
30	chr6:31026000-31034800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:31026200-31026600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:31026200-31026600	Enhancers	Hela-S3	cervix
33	chr6:31026200-31026600	Enhancers	NH-A	brain
34	chr6:31026200-31036200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:31026200-31038000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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