Variant report

Variant	rs7416659
Chromosome Location	chr1:246861685-246861686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246860479..246862658-chr1:246926455..246929333,2	MCF-7	breast:
2	chr1:246729662..246732533-chr1:246861048..246863453,2	MCF-7	breast:
3	chr1:246860463..246862143-chr1:246886118..246888895,2	MCF-7	breast:
4	chr1:246857655..246865600-chr1:246867157..246874213,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162852	Chromatin interaction
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10732299	1.00[AMR][1000 genomes]
rs10924822	1.00[AMR][1000 genomes]
rs12040914	1.00[AMR][1000 genomes]
rs12069175	1.00[AMR][1000 genomes]
rs12071299	1.00[AMR][1000 genomes]
rs2996552	1.00[AMR][1000 genomes]
rs3007320	1.00[AMR][1000 genomes]
rs3007321	1.00[AMR][1000 genomes]
rs3007325	1.00[AMR][1000 genomes]
rs3007326	1.00[AMR][1000 genomes]
rs3007327	1.00[AMR][1000 genomes]
rs4244625	1.00[AMR][1000 genomes]
rs4244626	1.00[AMR][1000 genomes]
rs4244629	1.00[AMR][1000 genomes]
rs4511163	1.00[AMR][1000 genomes]
rs4532864	1.00[AMR][1000 genomes]
rs4926452	1.00[AMR][1000 genomes]
rs4926463	1.00[AMR][1000 genomes]
rs6426335	1.00[AMR][1000 genomes]
rs6663093	1.00[AMR][1000 genomes]
rs6696798	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7364903	0.84[AFR][1000 genomes]
rs9426212	0.84[AFR][1000 genomes]
rs9426266	1.00[AMR][1000 genomes]
rs9426274	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246850600-246862400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:246853200-246862400	Weak transcription	Spleen	Spleen
3	chr1:246855600-246862000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:246855600-246862000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:246855600-246862000	Weak transcription	Psoas Muscle	Psoas
6	chr1:246855800-246862200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:246855800-246862400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:246855800-246862400	Weak transcription	Fetal Brain Male	brain
9	chr1:246860000-246861800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:246860000-246862000	Weak transcription	Fetal Heart	heart
11	chr1:246860000-246862000	Weak transcription	A549	lung
12	chr1:246860000-246862400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:246860200-246862000	Weak transcription	Esophagus	oesophagus
14	chr1:246860200-246862200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:246860200-246867400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:246860400-246861800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:246860400-246861800	Weak transcription	K562	blood
18	chr1:246860400-246862000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:246860400-246862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:246860400-246862000	Weak transcription	GM12878-XiMat	blood
21	chr1:246860400-246862000	Weak transcription	HSMM	muscle
22	chr1:246860400-246862000	Weak transcription	NH-A	brain
23	chr1:246860400-246862000	Weak transcription	Osteobl	bone
24	chr1:246860400-246862200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:246860400-246862200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:246860400-246862200	Weak transcription	Right Atrium	heart
27	chr1:246860400-246862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:246860400-246862400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:246860600-246861800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:246860600-246861800	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:246860600-246861800	Weak transcription	Lung	lung
32	chr1:246860600-246861800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:246860600-246861800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:246860600-246861800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:246860600-246861800	Weak transcription	HepG2	liver
36	chr1:246860600-246861800	Weak transcription	NHDF-Ad	bronchial
37	chr1:246860600-246862000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:246860600-246862000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:246860600-246862000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:246860600-246862000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:246860600-246862000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:246860600-246862000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:246860600-246862000	Weak transcription	Liver	Liver
44	chr1:246860600-246862000	Weak transcription	Colonic Mucosa	Colon
45	chr1:246860600-246862000	Weak transcription	Fetal Intestine Large	intestine
46	chr1:246860600-246862000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:246860600-246862000	Weak transcription	Left Ventricle	heart
48	chr1:246860600-246862000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:246860600-246862000	Weak transcription	HSMMtube	muscle
50	chr1:246860600-246862200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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