Variant report

Variant	rs13375555
Chromosome Location	chr1:173695225-173695226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173687895..173689585-chr1:173692482..173695234,2	MCF-7	breast:
2	chr1:173693597..173695637-chr1:173710759..173712908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225591	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10081990	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158663	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10798298	0.88[AMR][1000 genomes]
rs10912677	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912678	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912680	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912682	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912684	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1115487	0.88[AMR][1000 genomes]
rs11487392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065033	1.00[EUR][1000 genomes]
rs12067571	1.00[EUR][1000 genomes]
rs12070556	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12073601	1.00[EUR][1000 genomes]
rs12074150	1.00[EUR][1000 genomes]
rs12080389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082206	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12083423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085748	0.88[AMR][1000 genomes]
rs12085894	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12094130	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095090	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096832	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12098124	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322771	0.88[AMR][1000 genomes]
rs1322772	0.88[AMR][1000 genomes]
rs1474907	0.88[AMR][1000 genomes]
rs16846383	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16846420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2224657	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28578576	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs59845733	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6425257	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658217	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6663880	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670574	1.00[EUR][1000 genomes]
rs6675762	0.88[AMR][1000 genomes]
rs6686455	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6689764	0.88[AMR][1000 genomes]
rs6691327	0.88[AMR][1000 genomes]
rs6691922	0.88[AMR][1000 genomes]
rs6692452	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6695782	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6698348	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6702485	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518130	0.82[AMR][1000 genomes]
rs7522788	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7534521	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7536773	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7544583	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550036	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552840	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9282959	0.88[AMR][1000 genomes]
rs9282960	0.88[AMR][1000 genomes]
rs9286886	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286887	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286890	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286894	0.88[AMR][1000 genomes]
rs9425415	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425418	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425419	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425421	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425422	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425423	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425424	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425425	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425426	0.88[AMR][1000 genomes]
rs9425734	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425736	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425738	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425740	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425741	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425742	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425746	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425747	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425750	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425751	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425752	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425758	0.88[AMR][1000 genomes]
rs9425759	0.82[AMR][1000 genomes]
rs9425761	0.88[AMR][1000 genomes]
rs9442660	0.88[AMR][1000 genomes]
rs9970488	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9970633	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173684800-173702800	Weak transcription	Spleen	Spleen
2	chr1:173685000-173720800	Weak transcription	Small Intestine	intestine
3	chr1:173685200-173724600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:173685400-173702800	Weak transcription	Psoas Muscle	Psoas
5	chr1:173685400-173725000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:173685600-173702800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:173685800-173702800	Weak transcription	NH-A	brain
8	chr1:173685800-173703000	Weak transcription	Osteobl	bone
9	chr1:173685800-173724800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:173686200-173702800	Weak transcription	NHEK	skin
11	chr1:173686600-173702800	Weak transcription	HSMMtube	muscle
12	chr1:173686800-173702800	Weak transcription	Gastric	stomach
13	chr1:173686800-173703000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:173686800-173721600	Weak transcription	HUVEC	blood vessel
15	chr1:173686800-173721800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:173686800-173725400	Weak transcription	Right Ventricle	heart
17	chr1:173687000-173702800	Weak transcription	HepG2	liver
18	chr1:173687600-173706600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:173687800-173702200	Weak transcription	Lung	lung
20	chr1:173687800-173707200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:173689800-173695800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:173689800-173695800	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr1:173690600-173695600	ZNF genes & repeats	Fetal Brain Female	brain
24	chr1:173690600-173696200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:173690600-173696400	Strong transcription	Liver	Liver
26	chr1:173691200-173710000	Weak transcription	Hela-S3	cervix
27	chr1:173692200-173695800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:173692200-173696000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:173692200-173697000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr1:173692600-173695800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr1:173692600-173696000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:173692800-173696600	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr1:173693000-173702600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:173693200-173695400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:173693200-173695800	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr1:173693400-173696200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
37	chr1:173693600-173696000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:173693600-173696600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr1:173693800-173695400	Strong transcription	Adipose Nuclei	Adipose
40	chr1:173693800-173695600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
41	chr1:173693800-173695600	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr1:173693800-173695600	ZNF genes & repeats	Dnd41	blood
43	chr1:173693800-173695800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:173693800-173695800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:173693800-173695800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:173693800-173695800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:173693800-173695800	Strong transcription	Thymus	Thymus
48	chr1:173693800-173696000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr1:173693800-173696400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:173694000-173695600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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