Variant report

Variant	rs7896078
Chromosome Location	chr10:5652277-5652278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5637418..5639003-chr10:5650901..5653188,2	MCF-7	breast:
2	chr10:5486648..5491055-chr10:5645215..5653179,9	MCF-7	breast:
3	chr10:5634973..5639659-chr10:5649443..5654538,7	MCF-7	breast:
4	chr10:5651351..5653513-chr10:5657933..5661985,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASB13-2	chr10:5652277-5652399	XLOC_008712

Variant related genes	Relation type
ENSG00000173848	Chromatin interaction
ENSG00000228951	Chromatin interaction
ENSG00000242147	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10904531	0.85[ASN][1000 genomes]
rs10905112	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11255051	1.00[ASN][1000 genomes]
rs11255916	0.82[ASN][1000 genomes]
rs11259582	0.98[ASN][1000 genomes]
rs11259742	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1544216	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2380196	0.83[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2380197	0.84[ASN][1000 genomes]
rs2386663	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4747358	0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs57893347	0.97[ASN][1000 genomes]
rs61832660	0.81[ASN][1000 genomes]
rs61832676	0.97[ASN][1000 genomes]
rs61832677	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72781996	0.97[ASN][1000 genomes]
rs7896088	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7924096	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1036798	chr10:5637870-5652754	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1040932	chr10:5637870-5665774	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv466718	chr10:5639907-5657527	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv549890	chr10:5639907-5657527	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv894806	chr10:5643511-5670275	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1054888	chr10:5645033-5694612	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv466719	chr10:5645895-5662915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv549891	chr10:5645895-5662915	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv519582	chr10:5646103-5720067	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv894807	chr10:5647942-5691135	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv8599	chr10:5649129-5719928	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv1050965	chr10:5649760-5717125	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	nsv1044330	chr10:5652006-5717125	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	nsv975791	chr10:5652225-5711077	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
22	nsv466720	chr10:5652277-5715401	Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	nsv549892	chr10:5652277-5715401	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5649000-5657400	Weak transcription	Left Ventricle	heart
2	chr10:5650000-5653000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:5650200-5662600	Enhancers	Fetal Muscle Leg	muscle
4	chr10:5650400-5653000	Enhancers	NHDF-Ad	bronchial
5	chr10:5650400-5661800	Enhancers	Fetal Muscle Trunk	muscle
6	chr10:5650600-5652400	Enhancers	Aorta	Aorta
7	chr10:5650600-5653200	Enhancers	Liver	Liver
8	chr10:5650600-5653200	Enhancers	Fetal Intestine Small	intestine
9	chr10:5650800-5655600	Weak transcription	Adipose Nuclei	Adipose
10	chr10:5651000-5652400	Flanking Active TSS	HMEC	breast
11	chr10:5651200-5653400	Enhancers	Colonic Mucosa	Colon
12	chr10:5651200-5653400	Enhancers	Psoas Muscle	Psoas
13	chr10:5651200-5653600	Enhancers	Pancreas	Pancrea
14	chr10:5651200-5656000	Weak transcription	Fetal Lung	lung
15	chr10:5651400-5652400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:5651400-5652400	Flanking Active TSS	A549	lung
17	chr10:5651400-5652800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:5651400-5653000	Enhancers	Osteobl	bone
19	chr10:5651600-5652400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:5651600-5652400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr10:5651600-5652400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr10:5651600-5652400	Flanking Active TSS	Hela-S3	cervix
23	chr10:5651600-5652800	Flanking Active TSS	NHEK	skin
24	chr10:5651600-5653000	Enhancers	Gastric	stomach
25	chr10:5651600-5653200	Enhancers	HSMM	muscle
26	chr10:5651600-5653400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:5651600-5654200	Enhancers	HSMMtube	muscle
28	chr10:5651800-5652400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:5651800-5652400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr10:5651800-5653200	Enhancers	Stomach Smooth Muscle	stomach
31	chr10:5651800-5654400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr10:5651800-5654600	Enhancers	Stomach Mucosa	stomach
33	chr10:5651800-5655600	Weak transcription	Fetal Thymus	thymus
34	chr10:5651800-5655600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:5651800-5665000	Weak transcription	Spleen	Spleen
36	chr10:5652000-5652400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:5652000-5652400	Active TSS	Esophagus	oesophagus
38	chr10:5652000-5652600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr10:5652000-5653000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:5652000-5653000	Flanking Active TSS	HepG2	liver
41	chr10:5652000-5653200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr10:5652000-5654600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr10:5652200-5652400	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr10:5652200-5652400	Enhancers	NHLF	lung
45	chr10:5652200-5652800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr10:5652200-5652800	Weak transcription	Lung	lung
47	chr10:5652200-5655600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:5652200-5655600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr10:5652200-5655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:5652200-5655800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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