Variant report

Variant	rs7517108
Chromosome Location	chr1:228434467-228434468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228426358..228429102-chr1:228433065..228434825,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10737429	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916276	0.81[AMR][1000 genomes]
rs10916278	0.88[AMR][1000 genomes]
rs10916292	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916293	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188704	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188721	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1188722	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1188724	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12022917	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12026358	0.81[AMR][1000 genomes]
rs12047879	0.88[AMR][1000 genomes]
rs12142165	0.81[AMR][1000 genomes]
rs12741048	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12755546	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757130	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771455	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1771456	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1771457	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1888680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888681	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2150669	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2487384	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs287613	0.84[EUR][1000 genomes]
rs3795780	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4085473	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs450088	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653932	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533738	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6426493	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426494	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426495	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426496	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665929	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668967	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6677503	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517088	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526808	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529241	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532144	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535667	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878388	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936885	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs947084	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:228422200-228434800	ZNF genes & repeats	Dnd41	blood
3	chr1:228426000-228435200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr1:228427000-228435600	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr1:228427200-228434600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:228428200-228434600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:228428200-228435000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr1:228428400-228434600	ZNF genes & repeats	Liver	Liver
9	chr1:228428400-228434600	ZNF genes & repeats	Fetal Intestine Large	intestine
10	chr1:228428400-228435200	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr1:228428400-228436600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr1:228428600-228434600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
13	chr1:228428600-228434800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr1:228428600-228435000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
15	chr1:228428600-228435000	ZNF genes & repeats	Fetal Muscle Leg	muscle
16	chr1:228428800-228434800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr1:228429000-228434800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle
19	chr1:228430000-228435200	ZNF genes & repeats	Fetal Kidney	kidney
20	chr1:228430200-228434600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr1:228430200-228435000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:228430400-228434600	ZNF genes & repeats	Spleen	Spleen
23	chr1:228430400-228434800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr1:228430400-228434800	ZNF genes & repeats	Fetal Stomach	stomach
25	chr1:228430400-228435000	ZNF genes & repeats	A549	lung
26	chr1:228430400-228435200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:228430400-228435200	ZNF genes & repeats	Thymus	Thymus
28	chr1:228430400-228435800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:228430400-228436600	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:228430800-228434600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:228430800-228434600	ZNF genes & repeats	Fetal Thymus	thymus
33	chr1:228430800-228434800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:228430800-228435000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:228430800-228435000	ZNF genes & repeats	Esophagus	oesophagus
36	chr1:228430800-228435400	ZNF genes & repeats	Fetal Brain Female	brain
37	chr1:228430800-228440000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:228431000-228435400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:228431000-228436000	Strong transcription	Right Ventricle	heart
40	chr1:228431200-228439800	Strong transcription	Left Ventricle	heart
41	chr1:228431400-228436000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:228432000-228434600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr1:228432000-228434600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:228432000-228434800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr1:228432000-228435200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:228432000-228436800	Strong transcription	Psoas Muscle	Psoas
47	chr1:228432200-228434800	Strong transcription	Ovary	ovary
48	chr1:228432200-228435200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:228432200-228435400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:228432200-228435800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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