Variant report

Variant	rs2797780
Chromosome Location	chr6:37506415-37506416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37505637..37506607-chr6:37659097..37660191,6	MCF-7	breast:
2	chr6:37505588..37506541-chr6:37533884..37534986,5	MCF-7	breast:
3	chr6:37506023..37506547-chr6:37659493..37660057,3	K562	blood:
4	chr6:37477157..37479620-chr6:37505703..37507829,2	K562	blood:
5	chr6:37505189..37507848-chr6:37513483..37515469,2	K562	blood:
6	chr6:37497734..37501605-chr6:37502729..37507040,5	K562	blood:
7	chr6:37495218..37497669-chr6:37504507..37506713,2	K562	blood:
8	chr6:37479736..37486031-chr6:37501228..37507298,5	K562	blood:
9	chr6:37505371..37506520-chr6:37533735..37534780,10	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FTSJD2-1	chr6:37503308-37509148	XLOC_005278

No data

Variant related genes	Relation type
ENSG00000229559	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10947676	1.00[JPT][hapmap]
rs12201357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210274	1.00[JPT][hapmap]
rs12211948	1.00[JPT][hapmap]
rs16889902	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17574830	1.00[JPT][hapmap]
rs2776882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797779	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797782	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734319	1.00[JPT][hapmap]
rs62406767	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7774013	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1016310	chr6:37473075-37528469	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv462914	chr6:37502585-37517485	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602954	chr6:37502585-37517485	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2797780	FTSJD2	cis	parietal	SCAN
rs2797780	GPRASP1	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37493800-37514000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:37504200-37507600	Bivalent Enhancer	Fetal Thymus	thymus
3	chr6:37504200-37514000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:37504400-37507600	Enhancers	Fetal Brain Male	brain
5	chr6:37504400-37507600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr6:37504400-37513800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:37504400-37514200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:37504400-37515200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:37504400-37529200	Weak transcription	Right Atrium	heart
10	chr6:37504600-37508800	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:37505200-37515400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:37505800-37515400	Weak transcription	Fetal Brain Female	brain
13	chr6:37506200-37506600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:37506200-37506800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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