Variant report

Variant	rs9917673
Chromosome Location	chr3:150909872-150909873
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	chr3:150909405..150911951-chr3:150919073..150920609,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10513385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10513386	1.00[ASW][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12631155	0.81[ASW][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap]
rs12636713	0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1431494	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1431495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1431496	0.87[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863149	1.00[TSI][hapmap]
rs16863155	0.83[EUR][1000 genomes]
rs16863204	1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16863208	0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16863223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16863227	1.00[EUR][1000 genomes]
rs16863229	0.82[ASW][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863238	0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap]
rs16863248	0.82[ASW][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap]
rs2043170	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2870413	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs2870415	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs3732755	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732756	1.00[TSI][hapmap]
rs3773614	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs4330297	0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56151283	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56350229	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59669423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60749276	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61099669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440723	0.82[ASW][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap]
rs6772538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772543	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6775269	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6802229	0.87[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73016801	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73018604	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018614	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018621	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73018622	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73018628	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73018640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73018641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73019091	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7616375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650499	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650959	0.81[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
5	chr3:150889200-150914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:150889600-150913800	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:150890600-150923400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:150896200-150927800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:150896600-150918200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:150897200-150916200	Weak transcription	Fetal Intestine Small	intestine
11	chr3:150897600-150913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:150898600-150917200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:150899000-150917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:150900400-150910200	Weak transcription	Fetal Brain Female	brain
15	chr3:150900400-150917200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:150900600-150917000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:150900800-150917200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:150901200-150917600	Weak transcription	Fetal Thymus	thymus
19	chr3:150901200-150917800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:150901400-150910200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:150901400-150911600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:150901400-150914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:150901400-150916200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:150901600-150913600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:150901800-150918000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:150902200-150916400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:150904200-150911800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:150904600-150914000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:150904600-150914000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:150904600-150915200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:150904800-150911800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:150904800-150916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:150906000-150912400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr3:150907000-150917400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:150907200-150916200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:150907400-150915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:150907400-150916800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:150907800-150913200	Weak transcription	HepG2	liver
39	chr3:150908400-150911600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:150908800-150913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:150908800-150933200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:150909000-150917200	Weak transcription	Dnd41	blood
43	chr3:150909000-150918800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:150909200-150911400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:150909400-150913400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:150909600-150916200	Weak transcription	Fetal Intestine Large	intestine

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