Variant report

Variant	rs2736780
Chromosome Location	chr3:60066991-60066992
allele	C/T
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	RAD21	chr3:60066945-60067002	A549	lung:	n/a	n/a
2	TEAD4	chr3:60066732-60067050	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:60065873-60068059	Raji	blood:	n/a	n/a

Variant related genes	Relation type
FHIT	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2142300	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223086	0.87[CEU][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736784	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736785	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736786	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3920478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413275	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679628	0.95[CEU][hapmap]
rs7610403	0.81[JPT][hapmap]
rs7615700	0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7643042	0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs9817116	0.95[CEU][hapmap];0.81[AMR][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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60061800-60068400	Flanking Active TSS	Dnd41	blood
2	chr3:60063800-60068000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr3:60064600-60068400	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:60064800-60068000	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:60064800-60068000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:60065000-60067200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:60066000-60067200	Enhancers	Primary B cells from cord blood	blood
8	chr3:60066000-60067800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr3:60066000-60068200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr3:60066200-60067200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:60066200-60067200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:60066200-60067400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:60066200-60067400	Enhancers	Stomach Mucosa	stomach
14	chr3:60066200-60068200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr3:60066400-60067000	Flanking Active TSS	Thymus	Thymus
16	chr3:60066400-60067200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:60066400-60067200	Enhancers	Small Intestine	intestine
18	chr3:60066400-60067400	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:60066400-60068000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:60066400-60068200	Enhancers	GM12878-XiMat	blood
21	chr3:60066600-60067000	Enhancers	Brain Angular Gyrus	brain
22	chr3:60066600-60067000	Flanking Active TSS	Fetal Thymus	thymus
23	chr3:60066600-60067400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:60066600-60067800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:60066600-60068000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr3:60066800-60067000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:60066800-60067200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr3:60066800-60067200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:60066800-60068200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:60066800-60068600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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