Variant report

Variant	rs4317816
Chromosome Location	chr1:223125839-223125840
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223118299..223120802-chr1:223123598..223126411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234523	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11487819	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2378617	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2378618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378619	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2609359	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2609366	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609371	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2789910	0.90[AMR][1000 genomes]
rs2789924	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789929	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789931	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789933	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789934	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789937	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789945	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789953	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2789954	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789957	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2789958	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789972	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34188904	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34620158	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34673329	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4509582	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4846783	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837491	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67420224	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs728006	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs946506	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1828950	chr1:223111708-223132433	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 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	chr1:223102200-223128000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:223102200-223130800	Weak transcription	Fetal Brain Male	brain
3	chr1:223105000-223128800	Weak transcription	Ovary	ovary
4	chr1:223112600-223126200	Weak transcription	Osteobl	bone
5	chr1:223114200-223129000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:223114200-223130600	Weak transcription	Left Ventricle	heart
7	chr1:223114800-223129200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:223115200-223126600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:223116600-223126600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:223116800-223128200	Weak transcription	Placenta	Placenta
11	chr1:223116800-223130400	Weak transcription	Liver	Liver
12	chr1:223116800-223130600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:223116800-223135800	Weak transcription	Fetal Intestine Small	intestine
14	chr1:223117000-223126200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:223117000-223127000	Weak transcription	Fetal Brain Female	brain
16	chr1:223117000-223129200	Weak transcription	Brain Anterior Caudate	brain
17	chr1:223117000-223135000	Weak transcription	Primary B cells from cord blood	blood
18	chr1:223117000-223138400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:223117200-223127800	Weak transcription	Fetal Stomach	stomach
20	chr1:223117200-223133800	Weak transcription	Lung	lung
21	chr1:223119200-223131400	Weak transcription	Right Ventricle	heart
22	chr1:223120400-223126600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:223121000-223128000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:223123800-223127000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:223124200-223126800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:223124400-223128000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:223124400-223130400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:223125000-223126400	Weak transcription	Fetal Lung	lung
29	chr1:223125000-223131000	Weak transcription	Stomach Mucosa	stomach

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