Variant report

Variant	rs2797782
Chromosome Location	chr6:37504036-37504037
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	chr6:37497734..37501605-chr6:37502729..37507040,5	K562	blood:
2	chr6:37479736..37486031-chr6:37501228..37507298,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FTSJD2-1	chr6:37503308-37509148	XLOC_005278
2	lnc-FTSJD2-1	chr6:37503308-37506306	ENSG00000204110.5

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10947676	1.00[JPT][hapmap]
rs12201357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797779	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734319	1.00[JPT][hapmap]
rs62406767	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7774013	0.92[AMR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2797782	FTSJD2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

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	chr6:37502000-37504400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:37502800-37505800	Bivalent Enhancer	Fetal Lung	lung
4	chr6:37503200-37504200	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr6:37503200-37504200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
6	chr6:37503200-37504400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr6:37503200-37504400	Enhancers	Liver	Liver
8	chr6:37503200-37504400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
9	chr6:37503200-37504600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:37503200-37504600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:37503200-37504600	Bivalent Enhancer	Placenta	Placenta
12	chr6:37503200-37505000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr6:37503200-37505000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:37503400-37504200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
17	chr6:37503400-37504200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
18	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
20	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr6:37503400-37504200	Bivalent Enhancer	Esophagus	oesophagus
22	chr6:37503400-37504200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:37503400-37504200	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr6:37503400-37504200	Flanking Active TSS	GM12878-XiMat	blood
25	chr6:37503400-37504400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:37503400-37504400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:37503400-37504400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
28	chr6:37503400-37504400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:37503400-37504400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:37503400-37504400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
31	chr6:37503400-37504400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
32	chr6:37503400-37504600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:37503400-37504600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr6:37503400-37504600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:37503400-37504600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
36	chr6:37503400-37504600	Enhancers	Pancreas	Pancrea
37	chr6:37503400-37504600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
38	chr6:37503400-37504600	Flanking Active TSS	Right Ventricle	heart
39	chr6:37503400-37504800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:37503400-37504800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:37503400-37504800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:37503400-37504800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
43	chr6:37503400-37505000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr6:37503400-37505000	Bivalent Enhancer	Fetal Heart	heart
45	chr6:37503600-37504200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:37503600-37504200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:37503600-37504200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:37503600-37504200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr6:37503600-37504200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:37503600-37504200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

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