Variant report

Variant	rs4368477
Chromosome Location	chr3:43524407-43524408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43510126..43512612-chr3:43523954..43526015,2	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs17075519	0.93[AFR][1000 genomes]
rs17075525	0.93[AFR][1000 genomes]
rs17075540	0.93[AFR][1000 genomes]
rs17075545	0.90[AFR][1000 genomes]
rs17075555	0.90[AFR][1000 genomes]
rs17075561	0.90[AFR][1000 genomes]
rs17075563	0.90[AFR][1000 genomes]
rs17075564	0.88[AFR][1000 genomes]
rs17075568	0.90[AFR][1000 genomes]
rs17075570	0.90[AFR][1000 genomes]
rs17075574	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17075581	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17075587	0.90[AFR][1000 genomes]
rs17075614	0.88[AFR][1000 genomes]
rs17075617	0.82[AFR][1000 genomes]
rs17075623	0.88[AFR][1000 genomes]
rs17075624	0.88[AFR][1000 genomes]
rs17075696	0.94[AFR][1000 genomes]
rs17075709	1.00[AFR][1000 genomes]
rs17075750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075757	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs17075759	1.00[ASW][hapmap];1.00[LWK][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075762	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075773	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075776	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075780	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17075784	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17406718	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2036617	0.90[AFR][1000 genomes]
rs2086652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34343482	0.88[AFR][1000 genomes]
rs41321344	0.90[AFR][1000 genomes]
rs55692701	0.88[AFR][1000 genomes]
rs55760455	0.88[AFR][1000 genomes]
rs55765643	0.90[AFR][1000 genomes]
rs55804512	0.90[AFR][1000 genomes]
rs55823043	0.94[AFR][1000 genomes]
rs55837468	0.90[AFR][1000 genomes]
rs55864645	0.90[AFR][1000 genomes]
rs55887904	0.90[AFR][1000 genomes]
rs55908419	0.84[AFR][1000 genomes]
rs55919732	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55957435	0.90[AFR][1000 genomes]
rs55969335	0.94[AFR][1000 genomes]
rs56100043	0.90[AFR][1000 genomes]
rs56209592	1.00[AFR][1000 genomes]
rs56225070	0.90[AFR][1000 genomes]
rs56282728	0.88[AFR][1000 genomes]
rs56285372	0.87[AFR][1000 genomes]
rs56388016	0.90[AFR][1000 genomes]
rs56395291	0.82[AFR][1000 genomes]
rs56659864	0.90[AFR][1000 genomes]
rs56741341	0.90[AFR][1000 genomes]
rs56849726	1.00[AFR][1000 genomes]
rs57147822	0.94[AFR][1000 genomes]
rs57376786	0.90[AFR][1000 genomes]
rs58066802	1.00[AFR][1000 genomes]
rs58158782	0.88[AFR][1000 genomes]
rs58216554	0.88[AFR][1000 genomes]
rs58310281	0.94[AFR][1000 genomes]
rs58508138	0.90[AFR][1000 genomes]
rs58636339	0.90[AFR][1000 genomes]
rs58694029	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58866653	0.90[AFR][1000 genomes]
rs59113361	0.97[AFR][1000 genomes]
rs59121457	0.88[AFR][1000 genomes]
rs59276993	0.84[AFR][1000 genomes]
rs59423218	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59433561	1.00[AFR][1000 genomes]
rs59495244	0.97[AFR][1000 genomes]
rs59706458	0.90[AFR][1000 genomes]
rs60689590	0.90[AFR][1000 genomes]
rs60754038	0.94[AFR][1000 genomes]
rs61270592	0.90[AFR][1000 genomes]
rs61304871	1.00[AMR][1000 genomes]
rs61375879	0.90[AFR][1000 genomes]
rs6799735	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs73829503	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831224	0.84[AFR][1000 genomes]
rs73831230	0.84[AFR][1000 genomes]
rs73831233	0.90[AFR][1000 genomes]
rs73831234	0.90[AFR][1000 genomes]
rs73831236	0.90[AFR][1000 genomes]
rs73831237	0.90[AFR][1000 genomes]
rs73831238	0.90[AFR][1000 genomes]
rs73831239	0.90[AFR][1000 genomes]
rs73831240	0.90[AFR][1000 genomes]
rs73831241	0.90[AFR][1000 genomes]
rs73831243	0.90[AFR][1000 genomes]
rs73831244	0.90[AFR][1000 genomes]
rs73831245	0.90[AFR][1000 genomes]
rs73831247	0.90[AFR][1000 genomes]
rs73831248	0.90[AFR][1000 genomes]
rs73831249	0.90[AFR][1000 genomes]
rs73831250	0.90[AFR][1000 genomes]
rs73831251	0.90[AFR][1000 genomes]
rs73831252	0.90[AFR][1000 genomes]
rs73831253	0.90[AFR][1000 genomes]
rs73831256	0.85[AFR][1000 genomes]
rs73831261	0.90[AFR][1000 genomes]
rs73831267	0.90[AFR][1000 genomes]
rs73831273	0.88[AFR][1000 genomes]
rs73831274	0.88[AFR][1000 genomes]
rs73831275	0.88[AFR][1000 genomes]
rs73831277	0.81[AFR][1000 genomes]
rs73831279	0.82[AFR][1000 genomes]
rs73831280	0.88[AFR][1000 genomes]
rs73831281	0.88[AFR][1000 genomes]
rs73831283	0.88[AFR][1000 genomes]
rs73831285	0.88[AFR][1000 genomes]
rs73831287	0.97[AFR][1000 genomes]
rs73831288	1.00[AFR][1000 genomes]
rs73831291	1.00[AFR][1000 genomes]
rs73831292	1.00[AFR][1000 genomes]
rs73831294	1.00[AFR][1000 genomes]
rs73831295	1.00[AFR][1000 genomes]
rs73831296	1.00[AFR][1000 genomes]
rs73831297	1.00[AFR][1000 genomes]
rs73831301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832607	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832612	1.00[AMR][1000 genomes]
rs73832614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832616	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832620	0.94[AFR][1000 genomes]
rs73832622	0.94[AFR][1000 genomes]
rs73832625	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649808	1.00[AMR][1000 genomes]
rs984347	0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4368477	FLJ10375	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43473400-43541400	Weak transcription	Aorta	Aorta
2	chr3:43497000-43539400	Weak transcription	HSMM	muscle
3	chr3:43497200-43532600	Weak transcription	K562	blood
4	chr3:43504800-43553400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:43513000-43524600	Weak transcription	Psoas Muscle	Psoas
6	chr3:43515000-43526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:43515000-43532400	Weak transcription	Pancreas	Pancrea
8	chr3:43516000-43526600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:43519600-43539000	Weak transcription	Right Atrium	heart
10	chr3:43519800-43538200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:43521400-43526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:43522000-43532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:43522200-43525800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:43522200-43538200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:43522200-43538800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:43522400-43525600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:43522400-43539600	Weak transcription	HSMMtube	muscle
18	chr3:43523200-43525800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:43523200-43527800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:43523400-43527200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:43523400-43527400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:43523400-43531600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:43523600-43525800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:43523800-43524600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:43523800-43524600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:43523800-43524600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:43523800-43525000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:43523800-43526600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:43524000-43524600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:43524000-43524800	Enhancers	Primary T cells from cord blood	blood
31	chr3:43524000-43525000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:43524000-43525000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:43524000-43525000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:43524000-43525200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:43524000-43525200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:43524000-43525200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:43524000-43526000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:43524200-43525000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:43524200-43525800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:43524200-43539600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:43524400-43525000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:43524400-43526600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:43524400-43531000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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