Variant report

Variant	rs9262628
Chromosome Location	chr6:31023148-31023149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30710166..30712547-chr6:31022395..31024749,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 171 )
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]
rs2517523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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: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	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	esv3370627	chr6:31021373-31025571	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3473900	chr6:31023127-31023764	Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv15737	chr6:31023136-31023601	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9262628	HCG22	cis	Lymphoblastoid	GTEx
rs9262628	hmm31752	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 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	chr6:31022000-31023800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:31022200-31024600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:31022200-31024800	Weak transcription	Brain Germinal Matrix	brain
5	chr6:31022200-31025400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:31022200-31025400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:31022200-31025400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:31022200-31027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:31022400-31024200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:31022400-31024400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:31022400-31024800	Weak transcription	Brain Anterior Caudate	brain
13	chr6:31022400-31026600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:31022600-31026400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:31022600-31028200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:31022800-31026600	Enhancers	NHEK	skin

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