Variant report

Variant	rs10099941
Chromosome Location	chr8:95987008-95987009
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	chr8:95959150..95962570-chr8:95985356..95988577,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TP53INP1-3	chr8:95986801-95987081	NONHSAT127812

Variant related genes	Relation type
ENSG00000253878	Chromatin interaction
ENSG00000164938	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10081474	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10086284	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10097617	0.89[ASN][1000 genomes]
rs10098778	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10099059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10104909	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10108430	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1011795	0.94[JPT][hapmap]
rs1011796	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10429294	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10429443	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10441538	0.84[CHB][hapmap]
rs10808671	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10956929	0.85[CHB][hapmap]
rs10956930	0.93[CHB][hapmap]
rs10956931	1.00[CHB][hapmap]
rs10956932	1.00[CHB][hapmap]
rs10956933	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10956934	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1129152	0.86[CHB][hapmap]
rs11784717	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11996455	0.86[CHB][hapmap]
rs12386945	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548999	0.93[CHB][hapmap]
rs12549003	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12679044	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1320164	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13248607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255935	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13257021	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13262110	0.80[EUR][1000 genomes]
rs13266313	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13270641	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13271375	0.86[CHB][hapmap]
rs13274945	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13278601	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13281625	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13281709	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453377	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453379	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs16893776	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011566	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2123647	1.00[CHB][hapmap]
rs2340586	0.85[ASN][1000 genomes]
rs28560301	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28591375	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28716845	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2879813	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945554	1.00[CHB][hapmap]
rs2956210	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2956216	0.85[CHB][hapmap]
rs3019175	0.86[CHB][hapmap]
rs3802193	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4582532	0.86[ASN][1000 genomes]
rs4734291	0.82[JPT][hapmap]
rs4734295	0.81[CHB][hapmap]
rs4735328	0.85[CHB][hapmap]
rs4735331	0.93[CHB][hapmap]
rs4735332	0.93[CHB][hapmap]
rs4735333	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4735334	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs4735335	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735336	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735337	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735338	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4735339	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735340	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs477653	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs550418	0.86[CHB][hapmap]
rs550564	0.92[CHB][hapmap]
rs551270	0.85[CHB][hapmap]
rs61663478	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6471499	0.85[CHB][hapmap]
rs6471500	0.85[CHB][hapmap]
rs6471502	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471503	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471504	0.86[CHB][hapmap]
rs683832	0.92[CHB][hapmap]
rs6982393	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6983948	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6984240	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6987256	0.85[CHB][hapmap]
rs6987752	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6991067	0.86[CHB][hapmap]
rs7001535	0.93[CHB][hapmap]
rs7003387	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7004862	0.86[CHB][hapmap]
rs7005317	0.85[CHB][hapmap]
rs7015841	1.00[CHB][hapmap]
rs7017487	1.00[CHB][hapmap]
rs726816	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7815762	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7819800	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7820818	0.93[CHB][hapmap]
rs7823059	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827478	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7845219	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs896846	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896847	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896851	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs896852	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs896853	0.89[ASN][1000 genomes]
rs896854	0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs896855	0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297949	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9643353	0.85[CHB][hapmap];0.94[JPT][hapmap]

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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10099941	TP53INP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95964400-96002200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:95964600-95992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:95964800-95999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:95964800-95999600	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:95964800-95999600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:95965000-95999600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:95966000-95993000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr8:95970600-96000800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:95971400-95987400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:95971600-95987200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:95971600-96000400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:95972400-95994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr8:95972600-95987600	Weak transcription	HMEC	breast
14	chr8:95974400-96002000	Weak transcription	Esophagus	oesophagus
15	chr8:95976200-95990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:95976600-95993200	Weak transcription	Primary T cells from cord blood	blood
17	chr8:95976800-95988800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr8:95977400-95989600	Weak transcription	Fetal Stomach	stomach
19	chr8:95977400-96024200	Weak transcription	Aorta	Aorta
20	chr8:95977600-96008800	Weak transcription	Brain Germinal Matrix	brain
21	chr8:95980400-95993200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:95980800-95987200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:95980800-95988800	Weak transcription	Primary B cells from cord blood	blood
24	chr8:95980800-95993000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:95980800-95993000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:95980800-95993000	Weak transcription	HSMMtube	muscle
27	chr8:95980800-95993200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr8:95980800-95999400	Weak transcription	Brain Substantia Nigra	brain
29	chr8:95980800-95999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr8:95980800-96000200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr8:95980800-96000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr8:95981000-95988800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr8:95981000-95993000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:95981000-95993000	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:95981000-95999000	Weak transcription	Adipose Nuclei	Adipose
36	chr8:95981000-95999400	Weak transcription	Left Ventricle	heart
37	chr8:95981000-95999400	Weak transcription	Right Ventricle	heart
38	chr8:95981000-96000200	Weak transcription	NHLF	lung
39	chr8:95981000-96003000	Weak transcription	Fetal Lung	lung
40	chr8:95981200-95987600	Weak transcription	Fetal Thymus	thymus
41	chr8:95981200-95989400	Weak transcription	Fetal Intestine Large	intestine
42	chr8:95981200-95989600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:95981200-95994800	Weak transcription	Brain Anterior Caudate	brain
44	chr8:95981800-95994600	Weak transcription	Fetal Brain Female	brain
45	chr8:95981800-95999600	Weak transcription	Spleen	Spleen
46	chr8:95982000-95993000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr8:95982400-95993000	Weak transcription	Liver	Liver
48	chr8:95982600-95993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr8:95983600-95993200	Weak transcription	K562	blood
50	chr8:95983800-95989800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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