Variant report

Variant	rs56374740
Chromosome Location	chr2:54319517-54319518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54316883..54320439-chr2:54342176..54344468,4	MCF-7	breast:
2	chr2:54197521..54199570-chr2:54318251..54320315,2	MCF-7	breast:
3	chr2:54306094..54308840-chr2:54317877..54320671,2	K562	blood:
4	chr2:54314163..54315744-chr2:54319070..54321460,2	MCF-7	breast:
5	chr2:54319207..54320818-chr2:54338574..54340927,2	K562	blood:
6	chr2:54318413..54321728-chr2:54322663..54325829,3	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000241114	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10166363	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169648	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172916	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176342	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176406	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192403	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205315	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208690	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675345	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676433	1.00[ASN][1000 genomes]
rs11677951	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687470	1.00[ASN][1000 genomes]
rs11688581	1.00[ASN][1000 genomes]
rs11695936	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418039	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418658	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418839	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429859	0.86[EUR][1000 genomes]
rs1559039	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559040	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189638	1.00[ASN][1000 genomes]
rs2112125	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28368466	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416116	1.00[ASN][1000 genomes]
rs35641543	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666400	1.00[ASN][1000 genomes]
rs55672362	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55820614	1.00[ASN][1000 genomes]
rs61572658	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721034	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67951010	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799283	1.00[ASN][1000 genomes]
rs72799301	1.00[ASN][1000 genomes]
rs72800709	1.00[ASN][1000 genomes]
rs72800719	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800725	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800729	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800732	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800738	1.00[ASN][1000 genomes]
rs72800739	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800741	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800746	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800751	0.90[EUR][1000 genomes]
rs72800752	1.00[ASN][1000 genomes]
rs72800759	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800765	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800772	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800775	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571660	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586592	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998381	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
2	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:54305400-54321600	Weak transcription	Lung	lung
4	chr2:54311000-54324200	Weak transcription	HSMMtube	muscle
5	chr2:54315600-54319800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:54315600-54322600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:54315800-54319600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54315800-54319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:54315800-54319800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:54316200-54321800	Weak transcription	K562	blood
11	chr2:54316400-54319600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:54317800-54320000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:54318200-54319600	Enhancers	Primary B cells from cord blood	blood
14	chr2:54318200-54330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:54318200-54331000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:54318600-54319800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54318600-54319800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:54318800-54320400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:54319000-54320400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:54319000-54321800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:54319200-54320000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:54319200-54320200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:54319200-54321800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:54319400-54319800	Enhancers	GM12878-XiMat	blood
25	chr2:54319400-54320200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:54319400-54320200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr2:54319400-54320400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:54319400-54320400	Enhancers	Fetal Thymus	thymus
29	chr2:54319400-54320800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr2:54319400-54321400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:54319400-54321600	Enhancers	Primary T cells from cord blood	blood
32	chr2:54319400-54321800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:54319400-54322000	Enhancers	Primary T cells fromperipheralblood	blood

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