Variant report

Variant	rs17128099
Chromosome Location	chr10:112638393-112638394
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	chr10:112638388-112638404	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr10:112637932-112638930	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:112636674..112638811-chr10:112639092..112642951,4	MCF-7	breast:
2	chr10:112636714..112640059-chr10:112651978..112655187,3	K562	blood:
3	chr10:112630933..112635987-chr10:112638238..112642004,12	MCF-7	breast:
4	chr10:112582606..112584784-chr10:112635301..112639130,3	MCF-7	breast:

Variant related genes	Relation type
PDCD4	TF binding region
ENSG00000203867	Chromatin interaction
ENSG00000203497	Chromatin interaction
ENSG00000150593	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11195357	0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11195367	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11195378	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195384	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs11195389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195392	0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195393	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12240492	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12244153	0.85[AMR][1000 genomes]
rs12245003	1.00[YRI][hapmap]
rs12248431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12248632	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12248739	0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12255335	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12256152	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12258923	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12263197	0.81[AFR][1000 genomes]
rs12266042	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12267661	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12268160	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12268606	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1327552	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs1341055	0.90[AMR][1000 genomes]
rs1410052	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538998	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17128102	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128270	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3750621	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3750622	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3763691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4917593	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4918610	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55879225	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56005122	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56302131	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56350255	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9804245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112632800-112643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:112632800-112643800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:112632800-112678000	Weak transcription	Lung	lung
4	chr10:112632800-112678200	Weak transcription	Spleen	Spleen
5	chr10:112633200-112639000	Weak transcription	Gastric	stomach
6	chr10:112633200-112643800	Weak transcription	Esophagus	oesophagus
7	chr10:112633200-112643800	Weak transcription	Left Ventricle	heart
8	chr10:112633200-112656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:112633200-112656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:112633400-112662000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr10:112633600-112641000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:112633600-112641200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:112633600-112641200	Weak transcription	Brain Angular Gyrus	brain
14	chr10:112633600-112653800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr10:112633600-112655200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr10:112633800-112643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:112633800-112659800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr10:112634000-112638400	Weak transcription	NH-A	brain
19	chr10:112634000-112638600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr10:112634000-112638800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:112634000-112639000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:112634000-112639200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:112634000-112640800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:112634000-112641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:112634000-112641000	Weak transcription	Aorta	Aorta
26	chr10:112634000-112641000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr10:112634000-112643400	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:112634000-112643800	Weak transcription	Thymus	Thymus
29	chr10:112634000-112647000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr10:112634000-112649400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:112634000-112655000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:112634000-112655800	Weak transcription	Psoas Muscle	Psoas
33	chr10:112634000-112656000	Weak transcription	Right Ventricle	heart
34	chr10:112634000-112662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:112634200-112639600	Weak transcription	Stomach Mucosa	stomach
36	chr10:112634200-112639800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:112634200-112640400	Weak transcription	Colonic Mucosa	Colon
38	chr10:112634200-112643600	Weak transcription	Brain Germinal Matrix	brain
39	chr10:112634200-112643600	Weak transcription	Right Atrium	heart
40	chr10:112634200-112646600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:112634200-112655800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr10:112634400-112643200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr10:112634400-112643400	Weak transcription	NHLF	lung
44	chr10:112634600-112643400	Weak transcription	A549	lung
45	chr10:112634600-112656600	Weak transcription	NHEK	skin
46	chr10:112634800-112639200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:112634800-112639800	Weak transcription	Fetal Brain Female	brain
48	chr10:112634800-112641000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr10:112634800-112641000	Weak transcription	HSMMtube	muscle
50	chr10:112634800-112643400	Weak transcription	K562	blood

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