Variant report

Variant	rs17141003
Chromosome Location	chr3:46390839-46390840
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	EP300	chr3:46390409-46391079	T-47D	breast:	n/a	n/a
2	GATA3	chr3:46390444-46391254	T-47D	breast:	n/a	chr3:46391121-46391128 chr3:46391121-46391130 chr3:46391121-46391130 chr3:46391121-46391128 chr3:46391121-46391128 chr3:46391119-46391131 chr3:46391122-46391139 chr3:46391120-46391130 chr3:46391117-46391133 chr3:46391117-46391133
3	EP300	chr3:46390542-46390951	T-47D	breast:	n/a	n/a
4	FOXA1	chr3:46390533-46390860	T-47D	breast:	n/a	n/a
5	ESR1	chr3:46390567-46390938	T-47D	breast:	n/a	n/a
6	JUND	chr3:46390528-46391143	T-47D	breast:	n/a	n/a
7	ESR1	chr3:46390552-46390970	T-47D	breast:	n/a	n/a
8	GATA3	chr3:46390251-46391272	T-47D	breast:	n/a	chr3:46391121-46391128 chr3:46391121-46391130 chr3:46391121-46391130 chr3:46391121-46391128 chr3:46391121-46391128 chr3:46391119-46391131 chr3:46391122-46391139 chr3:46391120-46391130 chr3:46391117-46391133 chr3:46391117-46391133
9	SPI1	chr3:46390747-46391237	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46388161..46392582-chr3:46393253..46399062,5	K562	blood:
2	chr1:204096518..204097019-chr3:46390314..46391146,2	MCF-7	breast:

Variant related genes	Relation type
CCR2	TF binding region
ENSG00000121807	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11574431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574439	1.00[AMR][1000 genomes]
rs11574440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575814	1.00[EUR][1000 genomes]
rs11575817	1.00[EUR][1000 genomes]
rs11575818	1.00[EUR][1000 genomes]
rs11575822	1.00[EUR][1000 genomes]
rs13327723	1.00[EUR][1000 genomes]
rs17141076	1.00[EUR][1000 genomes]
rs17842821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17842822	1.00[EUR][1000 genomes]
rs2373253	1.00[EUR][1000 genomes]
rs3136536	1.00[EUR][1000 genomes]
rs3176763	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3181037	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35212534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3918370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41395345	1.00[EUR][1000 genomes]
rs41495153	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55951695	1.00[EUR][1000 genomes]
rs56062522	1.00[EUR][1000 genomes]
rs57509359	1.00[EUR][1000 genomes]
rs57761566	1.00[EUR][1000 genomes]
rs58966767	1.00[EUR][1000 genomes]
rs59998539	1.00[EUR][1000 genomes]
rs60350631	1.00[EUR][1000 genomes]
rs61737000	1.00[EUR][1000 genomes]
rs6441969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770833	1.00[EUR][1000 genomes]
rs6798819	1.00[EUR][1000 genomes]
rs6801203	1.00[EUR][1000 genomes]
rs723577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830784	1.00[EUR][1000 genomes]
rs73831107	1.00[EUR][1000 genomes]
rs7611447	1.00[EUR][1000 genomes]
rs7614209	1.00[EUR][1000 genomes]
rs7638702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640708	1.00[EUR][1000 genomes]
rs7650273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652954	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9282632	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46389200-46391400	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:46389400-46391200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:46389600-46391200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr3:46389600-46392400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:46390000-46391200	Enhancers	Primary B cells from cord blood	blood
6	chr3:46390000-46392800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:46390200-46391400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:46390200-46395000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:46390200-46395200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:46390200-46395200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:46390200-46396400	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:46390200-46397800	Enhancers	Fetal Thymus	thymus
13	chr3:46390400-46391800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:46390400-46391800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:46390400-46391800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:46390400-46392000	Flanking Active TSS	GM12878-XiMat	blood
17	chr3:46390400-46392400	Enhancers	Thymus	Thymus
18	chr3:46390400-46392400	Flanking Active TSS	Dnd41	blood
19	chr3:46390400-46392400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:46390600-46391200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:46390600-46391600	Weak transcription	Spleen	Spleen
22	chr3:46390600-46391800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr3:46390800-46391000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:46390800-46391200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:46390800-46391200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:46390800-46391200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:46390800-46391400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:46390800-46391800	Weak transcription	Placenta	Placenta
29	chr3:46390800-46391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:46390800-46392000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:46390800-46393000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:46390800-46396800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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