Variant report

Variant	rs1570385
Chromosome Location	chr1:173725878-173725879
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	chr1:173718954..173722251-chr1:173724534..173727033,3	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10157215	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157218	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157371	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157384	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157684	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158197	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158568	1.00[EUR][1000 genomes]
rs10399912	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489892	0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489893	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912668	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912687	0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912688	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912693	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912699	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912700	1.00[EUR][1000 genomes]
rs10912701	0.80[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10912707	1.00[EUR][1000 genomes]
rs10912708	1.00[EUR][1000 genomes]
rs10912711	1.00[EUR][1000 genomes]
rs10912712	1.00[EUR][1000 genomes]
rs1135333	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487390	1.00[EUR][1000 genomes]
rs12057440	0.89[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060967	0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061013	1.00[EUR][1000 genomes]
rs12062801	1.00[EUR][1000 genomes]
rs12063273	1.00[EUR][1000 genomes]
rs12063296	1.00[EUR][1000 genomes]
rs12064818	1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12078471	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078645	1.00[EUR][1000 genomes]
rs12079240	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079315	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079650	1.00[EUR][1000 genomes]
rs12081137	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083064	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084213	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086687	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12089398	0.86[LWK][hapmap]
rs12090440	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090507	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093624	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094912	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322773	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322781	0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16846278	0.95[LWK][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs16846395	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846398	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1903410	1.00[EUR][1000 genomes]
rs1903411	1.00[EUR][1000 genomes]
rs2227611	0.82[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2227622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28853918	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4652225	0.83[AMR][1000 genomes]
rs56195767	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57586767	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57820984	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59090917	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59332560	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60047664	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6425256	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684147	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690869	1.00[EUR][1000 genomes]
rs73033131	1.00[EUR][1000 genomes]
rs74126415	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550107	1.00[EUR][1000 genomes]
rs7556211	1.00[EUR][1000 genomes]
rs874342	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425414	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425427	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425735	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425768	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs997165	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv3598	chr1:173693027-173738687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173695400-173726000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:173695800-173726000	Weak transcription	Esophagus	oesophagus
3	chr1:173695800-173729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:173696200-173726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:173703400-173726000	Weak transcription	Aorta	Aorta
6	chr1:173703400-173726000	Weak transcription	Spleen	Spleen
7	chr1:173703400-173726000	Weak transcription	NHEK	skin
8	chr1:173703800-173728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:173710200-173726000	Weak transcription	Brain Germinal Matrix	brain
10	chr1:173713400-173731600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:173720000-173730000	Strong transcription	Primary B cells from cord blood	blood
12	chr1:173720000-173730600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:173720200-173727400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:173720200-173728000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:173720200-173729000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:173720200-173729000	Strong transcription	Dnd41	blood
17	chr1:173720200-173729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:173720200-173729800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:173720200-173730000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:173720200-173730200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:173720400-173726000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:173720400-173727000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:173720400-173729800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:173720600-173728000	Weak transcription	Stomach Mucosa	stomach
25	chr1:173720600-173728600	Strong transcription	Hela-S3	cervix
26	chr1:173720600-173729000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:173720800-173727200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr1:173720800-173728800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:173720800-173728800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:173720800-173728800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:173720800-173729000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:173720800-173729000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr1:173720800-173729200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173720800-173729400	Strong transcription	Primary T cells from cord blood	blood
35	chr1:173720800-173729600	Strong transcription	Adipose Nuclei	Adipose
36	chr1:173720800-173729800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:173720800-173729800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:173720800-173729800	Strong transcription	Fetal Thymus	thymus
39	chr1:173720800-173730000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:173720800-173730000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:173721000-173727400	Strong transcription	Fetal Intestine Small	intestine
42	chr1:173721000-173728200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:173721000-173729000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:173721000-173729600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:173721000-173730400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:173721200-173728200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:173721200-173730200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:173721400-173727600	Strong transcription	HSMM	muscle
49	chr1:173721400-173728000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:173721400-173729200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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