Variant report

Variant	rs11916224
Chromosome Location	chr3:28387575-28387576
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	chr3:28387500-28387623	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr3:28387455-28387632	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28370043..28372109-chr3:28386223..28389083,2	MCF-7	breast:

Variant related genes	Relation type
ZCWPW2	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11918573	0.91[YRI][hapmap]
rs11918809	0.83[AMR][1000 genomes]
rs11919446	1.00[EUR][1000 genomes]
rs11923033	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11923748	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs11926821	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs55758484	1.00[EUR][1000 genomes]
rs55817728	1.00[EUR][1000 genomes]
rs55962685	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56082224	1.00[EUR][1000 genomes]
rs56199335	1.00[EUR][1000 genomes]
rs57400334	1.00[EUR][1000 genomes]
rs57850842	1.00[EUR][1000 genomes]
rs60023459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60355399	1.00[EUR][1000 genomes]
rs61588415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794482	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6800120	0.89[LWK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6800367	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6804419	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73822335	0.83[AMR][1000 genomes]
rs73822569	0.85[AMR][1000 genomes]
rs73822571	0.85[AMR][1000 genomes]
rs73822575	0.85[AMR][1000 genomes]
rs73822579	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73822639	1.00[EUR][1000 genomes]
rs73822644	1.00[EUR][1000 genomes]
rs73822646	1.00[EUR][1000 genomes]
rs73822647	1.00[EUR][1000 genomes]
rs73823977	1.00[EUR][1000 genomes]
rs73823978	1.00[EUR][1000 genomes]
rs73823979	1.00[EUR][1000 genomes]
rs73823980	1.00[EUR][1000 genomes]
rs73823981	1.00[EUR][1000 genomes]
rs73823982	1.00[EUR][1000 genomes]
rs73823983	1.00[EUR][1000 genomes]
rs73823984	1.00[EUR][1000 genomes]
rs73823985	1.00[EUR][1000 genomes]
rs73823986	1.00[EUR][1000 genomes]
rs73823988	1.00[EUR][1000 genomes]
rs73825125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825141	0.90[AFR][1000 genomes]
rs73825145	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73825155	1.00[EUR][1000 genomes]
rs73825158	1.00[EUR][1000 genomes]
rs73825159	1.00[EUR][1000 genomes]
rs73825160	1.00[EUR][1000 genomes]
rs73825164	1.00[EUR][1000 genomes]
rs7627778	1.00[EUR][1000 genomes]
rs7628073	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649677	1.00[YRI][hapmap];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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
2	chr3:28349800-28389400	Weak transcription	Gastric	stomach
3	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
5	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
7	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
8	chr3:28365400-28389400	Weak transcription	Lung	lung
9	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
11	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
15	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
17	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:28368400-28387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:28368400-28388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:28372400-28388400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:28373400-28388400	Weak transcription	Stomach Mucosa	stomach
22	chr3:28374000-28387800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:28377800-28387600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:28377800-28387600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:28377800-28388600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:28377800-28389200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:28378400-28389400	Weak transcription	Ovary	ovary
28	chr3:28379000-28389600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:28379200-28387800	Weak transcription	Psoas Muscle	Psoas
30	chr3:28379200-28388200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:28379400-28388800	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:28379600-28387800	Weak transcription	Primary B cells from cord blood	blood
33	chr3:28380200-28387600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:28380600-28388400	Weak transcription	Fetal Intestine Large	intestine
35	chr3:28380600-28388400	Weak transcription	HSMMtube	muscle
36	chr3:28380600-28389200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr3:28380800-28387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:28380800-28388800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:28380800-28388800	Weak transcription	Left Ventricle	heart
40	chr3:28380800-28389200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:28381200-28388800	Weak transcription	Fetal Thymus	thymus
42	chr3:28381600-28389200	Weak transcription	Placenta	Placenta
43	chr3:28381800-28388200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:28381800-28388400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:28381800-28388600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:28381800-28388800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:28382000-28388400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:28382200-28388400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:28382200-28388600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:28382800-28388800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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