Variant report

Variant	rs10489893
Chromosome Location	chr1:173756803-173756804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:173756440-173757581	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173754859..173757504-chr1:173792732..173795086,3	K562	blood:
2	chr1:173753678..173758387-chr1:173760653..173764131,5	K562	blood:
3	chr1:173754859..173757077-chr1:173792732..173794871,2	K562	blood:

Variant related genes	Relation type
RN7SKP160	TF binding region
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000200674	Chromatin interaction

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

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

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];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912668	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912674	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912687	0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912688	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912693	0.95[YRI][hapmap];0.85[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	0.87[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	0.80[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12064818	1.00[EUR][1000 genomes]
rs12065194	1.00[EUR][1000 genomes]
rs12067109	1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12068440	1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12072553	1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12078471	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078645	1.00[EUR][1000 genomes]
rs12078817	1.00[EUR][1000 genomes]
rs12079240	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079315	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079650	1.00[TSI][hapmap];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];0.81[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];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084213	0.94[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];0.89[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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322773	1.00[YRI][hapmap];0.90[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]
rs1570385	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]
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	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57586767	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57820984	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59090917	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59332560	0.82[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	0.86[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	0.85[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: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	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173726200-173760600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:173728800-173764800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:173729800-173781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:173735800-173781000	Weak transcription	Small Intestine	intestine
5	chr1:173736600-173792400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:173736800-173760600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:173741400-173757400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:173741800-173759600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:173741800-173762400	Weak transcription	Stomach Mucosa	stomach
10	chr1:173742800-173759800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:173743200-173757200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:173743200-173758800	Strong transcription	Primary T cells from cord blood	blood
13	chr1:173743400-173757200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:173743400-173757200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:173743400-173757400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:173743400-173757800	Strong transcription	Dnd41	blood
17	chr1:173743400-173758000	Strong transcription	Fetal Thymus	thymus
18	chr1:173744800-173790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:173745000-173767400	Weak transcription	NHEK	skin
20	chr1:173745000-173792400	Weak transcription	Psoas Muscle	Psoas
21	chr1:173745200-173765200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:173745800-173759600	Strong transcription	Liver	Liver
23	chr1:173746800-173757200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:173746800-173757200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:173746800-173757200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:173747200-173757200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:173747400-173757200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:173747800-173769200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:173748600-173757200	Strong transcription	Placenta	Placenta
30	chr1:173748600-173757400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:173748600-173759000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:173748800-173757600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:173748800-173757600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:173749000-173757200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:173749000-173757600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:173749200-173792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:173749800-173758200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:173749800-173777800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:173750200-173757200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:173750400-173758800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:173750600-173760800	Weak transcription	Fetal Heart	heart
42	chr1:173750800-173757600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:173751200-173757200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:173751200-173773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:173751400-173757600	Strong transcription	Osteobl	bone
46	chr1:173751400-173759600	Strong transcription	HSMM	muscle
47	chr1:173751400-173769000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:173751400-173792200	Weak transcription	Fetal Kidney	kidney
49	chr1:173751800-173774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:173752600-173790000	Weak transcription	HepG2	liver

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