Variant report

Variant	rs10486798
Chromosome Location	chr7:39650450-39650451
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	chr7:39649814..39652615-chr7:39661583..39664092,3	MCF-7	breast:
2	chr7:39650430..39653003-chr7:39667356..39670007,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YAE1D1-1	chr7:39649086-39651687	NONHSAT120210

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10245247	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258946	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266149	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12111908	0.98[ASN][1000 genomes]
rs17171603	0.82[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.82[ASN][1000 genomes]
rs17713951	0.86[ASN][1000 genomes]
rs17714049	0.98[ASN][1000 genomes]
rs17770594	0.82[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17770625	0.82[ASN][1000 genomes]
rs1989533	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329460	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329461	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4451213	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4469364	0.90[AFR][1000 genomes]
rs4720329	0.93[AFR][1000 genomes]
rs4723881	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299139	0.82[ASN][1000 genomes]
rs59071947	0.82[ASN][1000 genomes]
rs61493712	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958662	0.94[AFR][1000 genomes]
rs6968742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375695	0.82[ASN][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7785964	0.82[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]
rs7809088	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39645200-39661600	Weak transcription	A549	lung
2	chr7:39648400-39651800	Flanking Active TSS	HUVEC	blood vessel
3	chr7:39648800-39656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:39649400-39652800	Weak transcription	Osteobl	bone
5	chr7:39649400-39654600	Weak transcription	Pancreas	Pancrea
6	chr7:39649600-39653400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:39649600-39655400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:39649600-39655600	Weak transcription	HSMMtube	muscle
9	chr7:39649800-39651000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:39649800-39651200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:39649800-39651200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:39649800-39651400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:39649800-39653600	Weak transcription	HSMM	muscle
14	chr7:39649800-39655000	Weak transcription	Hela-S3	cervix
15	chr7:39649800-39655200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:39649800-39655200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:39649800-39655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:39650000-39651800	Weak transcription	Gastric	stomach
19	chr7:39650000-39652600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:39650000-39653200	Weak transcription	NHDF-Ad	bronchial
21	chr7:39650000-39653400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:39650000-39653400	Weak transcription	NH-A	brain
23	chr7:39650000-39653600	Weak transcription	K562	blood
24	chr7:39650000-39654800	Weak transcription	Stomach Mucosa	stomach
25	chr7:39650000-39655000	Weak transcription	NHLF	lung
26	chr7:39650200-39651800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:39650200-39655400	Weak transcription	HMEC	breast
28	chr7:39650400-39652400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:39650400-39653200	Weak transcription	NHEK	skin

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