Variant report

Variant	rs7538745
Chromosome Location	chr1:171499994-171499995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171492212..171494194-chr1:171499059..171501581,2	MCF-7	breast:
2	chr1:171497816..171500280-chr1:171502329..171504189,2	MCF-7	breast:
3	chr1:171454073..171454798-chr1:171499804..171500717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1055417	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913167	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119596	0.81[ASN][1000 genomes]
rs12129856	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12131694	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12136576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137832	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139715	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142594	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145045	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145085	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12146022	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12733939	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12734261	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759907	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs171005	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs183533	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs190198	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294292	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294293	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235471	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235472	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235477	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs235488	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235495	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235498	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235502	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235507	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235865	0.85[ASN][1000 genomes]
rs235886	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235892	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235893	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235895	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235897	0.85[EUR][1000 genomes]
rs235898	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235899	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235900	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235901	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235902	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235903	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235904	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235910	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235911	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235912	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28661007	0.85[ASN][1000 genomes]
rs46407	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs536753	0.85[ASN][1000 genomes]
rs559739	0.85[ASN][1000 genomes]
rs56207586	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs591286	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631259	0.85[ASN][1000 genomes]
rs67133611	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71637410	0.91[EUR][1000 genomes]
rs71637418	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71637419	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74122850	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171475800-171524400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:171481000-171528000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:171481200-171518800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:171481200-171519200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:171481200-171519600	Strong transcription	Dnd41	blood
6	chr1:171481200-171520000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:171481200-171522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:171481400-171519200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:171481400-171519800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:171481400-171520000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:171481400-171522800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:171481600-171519200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:171481600-171520600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:171481800-171520000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:171481800-171520600	Strong transcription	Placenta	Placenta
16	chr1:171482000-171519800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:171482000-171520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:171482000-171520400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:171482000-171520400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr1:171482000-171522000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:171482000-171523000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:171482000-171524400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:171482200-171506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:171482200-171508200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:171482200-171512000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:171482200-171518400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:171482200-171519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:171482200-171520000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:171482200-171520000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:171482200-171520400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:171482200-171520600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:171482200-171520600	Strong transcription	Fetal Thymus	thymus
33	chr1:171482200-171541800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:171482400-171503200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:171482400-171520000	Strong transcription	Liver	Liver
36	chr1:171482400-171520400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:171482600-171520600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:171483200-171505800	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:171483200-171513800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:171483200-171520400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:171483200-171520600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:171483600-171503400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:171483600-171513200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:171483600-171520400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:171483800-171501800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:171485200-171513800	Strong transcription	Fetal Intestine Large	intestine
47	chr1:171486800-171509200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:171489800-171502600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:171490400-171502600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:171490600-171501800	Strong transcription	Thymus	Thymus

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