Variant report

Variant	rs10486183
Chromosome Location	chr7:7604599-7604600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr7:7603709-7604640	MCF-7	breast:	n/a	n/a
2	SMARCC1	chr7:7603662-7604948	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr7:7603649-7604751	IMR90	lung:	n/a	n/a
4	RCOR1	chr7:7604585-7605090	K562	blood:	n/a	n/a
5	TCF7L2	chr7:7603866-7604653	HCT-116	colon:	n/a	chr7:7604074-7604084 chr7:7604072-7604086
6	SPI1	chr7:7604051-7604851	HL-60	blood:	n/a	n/a
7	JUND	chr7:7603487-7604753	SK-N-SH	brain:	n/a	chr7:7604137-7604148

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7603096..7605323-chr7:7605419..7606942,2	MCF-7	breast:
2	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272894	TF binding region
MIOS	TF binding region
ENSG00000219545	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10235484	0.87[EUR][1000 genomes]
rs10276699	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486184	0.83[AMR][1000 genomes]
rs11972066	0.86[EUR][1000 genomes]
rs11984435	0.86[EUR][1000 genomes]
rs12666084	0.86[EUR][1000 genomes]
rs12666106	0.86[EUR][1000 genomes]
rs12666212	0.86[EUR][1000 genomes]
rs12669035	0.86[EUR][1000 genomes]
rs12670328	0.86[EUR][1000 genomes]
rs12671201	0.86[EUR][1000 genomes]
rs12671418	0.86[EUR][1000 genomes]
rs12672583	0.86[EUR][1000 genomes]
rs17151551	0.90[AFR][1000 genomes]
rs17167726	0.86[EUR][1000 genomes]
rs17167748	0.86[EUR][1000 genomes]
rs17167774	0.86[EUR][1000 genomes]
rs17167927	0.86[EUR][1000 genomes]
rs17168444	0.90[AFR][1000 genomes]
rs17168526	0.90[AFR][1000 genomes]
rs17168704	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169036	0.83[AMR][1000 genomes]
rs17457863	0.86[EUR][1000 genomes]
rs17459718	0.86[EUR][1000 genomes]
rs17459836	0.86[EUR][1000 genomes]
rs17459995	0.86[EUR][1000 genomes]
rs17460037	0.86[EUR][1000 genomes]
rs17461022	0.86[EUR][1000 genomes]
rs17461446	0.86[EUR][1000 genomes]
rs17461474	0.86[EUR][1000 genomes]
rs17461538	0.86[EUR][1000 genomes]
rs17462749	0.86[EUR][1000 genomes]
rs17462946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17464497	1.00[AMR][1000 genomes]
rs17464517	1.00[AMR][1000 genomes]
rs17464585	1.00[AMR][1000 genomes]
rs17465493	1.00[AMR][1000 genomes]
rs17516587	0.86[EUR][1000 genomes]
rs17516628	0.86[EUR][1000 genomes]
rs17516739	0.86[EUR][1000 genomes]
rs17517530	0.86[EUR][1000 genomes]
rs17518933	0.86[EUR][1000 genomes]
rs17519339	0.86[EUR][1000 genomes]
rs17519423	0.86[EUR][1000 genomes]
rs17519676	0.86[EUR][1000 genomes]
rs17520004	0.86[EUR][1000 genomes]
rs17520619	0.86[EUR][1000 genomes]
rs17520689	0.86[EUR][1000 genomes]
rs17521499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521779	0.86[EUR][1000 genomes]
rs17521814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522036	0.86[EUR][1000 genomes]
rs17522077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522279	0.86[EUR][1000 genomes]
rs17522625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522950	0.86[EUR][1000 genomes]
rs17523400	0.86[EUR][1000 genomes]
rs1860726	0.86[EUR][1000 genomes]
rs1922629	0.86[EUR][1000 genomes]
rs1978190	0.89[ASN][1000 genomes]
rs2191815	0.86[EUR][1000 genomes]
rs34330034	0.86[EUR][1000 genomes]
rs35473859	0.86[EUR][1000 genomes]
rs35772304	0.86[EUR][1000 genomes]
rs3757531	1.00[ASN][1000 genomes]
rs3757532	1.00[ASN][1000 genomes]
rs58901081	1.00[AFR][1000 genomes]
rs60654515	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956575	1.00[AFR][1000 genomes]
rs6957976	1.00[ASN][1000 genomes]
rs6969871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73674556	0.86[EUR][1000 genomes]
rs7778775	0.83[AMR][1000 genomes]
rs7782178	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783489	0.93[YRI][hapmap];0.98[AFR][1000 genomes]
rs7791080	0.98[AFR][1000 genomes]
rs7796098	0.93[YRI][hapmap];0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
3	chr7:7590000-7606200	Weak transcription	Ovary	ovary
4	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:7593800-7606000	Weak transcription	Right Atrium	heart
7	chr7:7595800-7605600	Weak transcription	Fetal Kidney	kidney
8	chr7:7597000-7605400	Weak transcription	Lung	lung
9	chr7:7597200-7606600	Weak transcription	Gastric	stomach
10	chr7:7597800-7606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:7599200-7605800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:7600000-7606000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:7601600-7605000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:7602200-7604600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:7602200-7605800	Enhancers	Liver	Liver
16	chr7:7602400-7605800	Enhancers	Stomach Mucosa	stomach
17	chr7:7602600-7605000	Enhancers	Placenta	Placenta
18	chr7:7602800-7606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:7603000-7605200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr7:7603000-7605800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr7:7603200-7604800	Enhancers	Fetal Intestine Small	intestine
22	chr7:7603400-7606000	Enhancers	HMEC	breast
23	chr7:7603600-7604600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr7:7603600-7604600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:7603600-7604600	Enhancers	Fetal Intestine Large	intestine
26	chr7:7603600-7604600	Enhancers	NH-A	brain
27	chr7:7603600-7604800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:7603600-7604800	Enhancers	HSMMtube	muscle
29	chr7:7603600-7604800	Enhancers	K562	blood
30	chr7:7603600-7604800	Enhancers	Osteobl	bone
31	chr7:7603600-7605400	Enhancers	NHDF-Ad	bronchial
32	chr7:7603600-7605800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr7:7603600-7606200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:7603600-7606400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr7:7603800-7604600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr7:7603800-7604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:7603800-7605400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:7603800-7605400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:7603800-7605400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:7603800-7605800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:7603800-7605800	Weak transcription	HepG2	liver
42	chr7:7603800-7606000	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:7603800-7606000	Enhancers	HSMM	muscle
44	chr7:7604000-7604600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:7604000-7604600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:7604000-7605000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr7:7604000-7605800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:7604200-7604600	Flanking Active TSS	A549	lung
49	chr7:7604200-7605800	Weak transcription	Psoas Muscle	Psoas
50	chr7:7604200-7606000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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