Variant report

Variant	rs6874227
Chromosome Location	chr5:118468658-118468659
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	POLR2A	chr5:118468385-118469099	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118465720..118469192-chr5:118469871..118473875,5	K562	blood:
2	chr5:118463365..118465367-chr5:118467203..118470688,3	K562	blood:

Variant related genes	Relation type
DMXL1	TF binding region
LAMTOR3P2	TF binding region
ENSG00000248885	TF binding region
ENSG00000172869	Chromatin interaction
ENSG00000248885	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10056088	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs10900728	0.90[ASN][1000 genomes]
rs11241482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs11241486	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11241492	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11241496	0.89[YRI][hapmap]
rs11738650	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12188483	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12516300	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518168	0.90[ASN][1000 genomes]
rs12653377	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12653870	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12657132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs12659055	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13189818	1.00[JPT][hapmap]
rs1553544	1.00[ASW][hapmap];0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2036565	0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs3822516	0.82[MEX][hapmap]
rs3923326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3992621	0.90[ASN][1000 genomes]
rs4565243	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4583917	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs4639262	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs57278208	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60504316	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62374138	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6595174	0.89[TSI][hapmap]
rs6595176	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6863826	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6866260	0.82[YRI][hapmap]
rs6880622	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs6887690	0.89[YRI][hapmap]
rs6893733	1.00[JPT][hapmap]
rs6894429	1.00[JPT][hapmap]
rs7702867	0.91[GIH][hapmap]
rs7706218	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7713483	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7727906	0.89[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs9790885	0.81[AMR][1000 genomes];0.90[EUR][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	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118409000-118471200	Weak transcription	Gastric	stomach
2	chr5:118412200-118522800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:118414400-118472200	Weak transcription	Pancreas	Pancrea
4	chr5:118415400-118471600	Weak transcription	Right Ventricle	heart
5	chr5:118430200-118471400	Weak transcription	Colonic Mucosa	Colon
6	chr5:118430800-118472200	Weak transcription	Esophagus	oesophagus
7	chr5:118431000-118472200	Weak transcription	Small Intestine	intestine
8	chr5:118434200-118471000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:118438600-118484400	Weak transcription	NHLF	lung
10	chr5:118442200-118472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:118443200-118472200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:118444000-118472000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:118444800-118471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:118447400-118485400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:118448800-118471600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:118450400-118496800	Weak transcription	Stomach Mucosa	stomach
17	chr5:118451200-118533400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:118452600-118468800	Weak transcription	NHDF-Ad	bronchial
19	chr5:118452800-118472400	Weak transcription	Hela-S3	cervix
20	chr5:118453000-118472400	Weak transcription	Psoas Muscle	Psoas
21	chr5:118453600-118471200	Weak transcription	Aorta	Aorta
22	chr5:118453800-118522800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:118454200-118468800	Weak transcription	Osteobl	bone
24	chr5:118456800-118469200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:118456800-118483200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:118456800-118484600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:118457000-118471200	Weak transcription	Lung	lung
28	chr5:118457000-118472200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:118457000-118472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:118458800-118470600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:118459400-118471000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:118459600-118471200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:118459600-118471200	Weak transcription	Spleen	Spleen
34	chr5:118460200-118468800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:118460200-118469200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:118460800-118471000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:118461600-118470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:118462800-118470800	Strong transcription	Dnd41	blood
39	chr5:118463400-118468800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:118463400-118469200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:118463600-118471600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:118463800-118470600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:118464000-118473400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:118464200-118469000	Strong transcription	GM12878-XiMat	blood
45	chr5:118464400-118469600	Weak transcription	Brain Substantia Nigra	brain
46	chr5:118464600-118471000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:118464800-118471200	Weak transcription	Fetal Stomach	stomach
48	chr5:118465400-118469200	Weak transcription	Placenta	Placenta
49	chr5:118465600-118469200	Weak transcription	NH-A	brain
50	chr5:118465600-118483000	Weak transcription	HUVEC	blood vessel

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