Variant report

Variant	rs6880622
Chromosome Location	chr5:118464075-118464076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118463365..118465744-chr5:118468945..118471414,3	K562	blood:
2	chr5:118463365..118465367-chr5:118467203..118470688,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DTWD2-7	chr5:118463435-118464139	NONHSAT103421
2	lnc-TNFAIP8-8	chr5:118463897-118464783	NONHSAT103422

Variant related genes	Relation type
ENSG00000248979	Chromatin interaction
ENSG00000172869	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10052879	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10064311	1.00[JPT][hapmap]
rs10065628	0.85[ASN][1000 genomes]
rs10071407	1.00[JPT][hapmap]
rs10900727	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11241489	0.90[ASN][1000 genomes]
rs11241490	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11241492	0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs11241498	0.80[ASN][1000 genomes]
rs11738702	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12516300	0.81[TSI][hapmap]
rs12653870	1.00[CHD][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs12658987	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1394629	1.00[JPT][hapmap]
rs1553544	0.84[TSI][hapmap]
rs299192	1.00[JPT][hapmap]
rs3923326	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs4286709	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4380699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4512152	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4533918	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4583917	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4895185	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs57278208	0.86[ASN][1000 genomes]
rs61279074	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62374136	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6595174	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6595176	0.82[CEU][hapmap]
rs6595178	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6595179	0.85[ASN][1000 genomes]
rs6863826	1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs6874227	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs6874843	0.85[CEU][hapmap]
rs6889308	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6893733	1.00[JPT][hapmap]
rs6894997	1.00[JPT][hapmap]
rs7702867	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs7713483	0.86[ASN][1000 genomes]
rs7720231	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs7734532	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7736400	1.00[JPT][hapmap]
rs9327087	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9327093	1.00[JPT][hapmap]
rs9790885	1.00[CHD][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6880622	DTWD2	cis	parietal	SCAN

Chromatin state (count:119 , 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	chr5:118433000-118466800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:118433000-118468600	Weak transcription	Fetal Heart	heart
10	chr5:118434200-118471000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:118438600-118484400	Weak transcription	NHLF	lung
12	chr5:118442000-118465200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:118442200-118472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:118442400-118465200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:118443200-118472200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:118444000-118472000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:118444800-118471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:118445600-118467200	Weak transcription	A549	lung
19	chr5:118447400-118485400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:118448800-118471600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:118450400-118496800	Weak transcription	Stomach Mucosa	stomach
22	chr5:118451200-118533400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:118452400-118465000	Weak transcription	Fetal Brain Male	brain
24	chr5:118452600-118465000	Weak transcription	HSMM	muscle
25	chr5:118452600-118468800	Weak transcription	NHDF-Ad	bronchial
26	chr5:118452800-118472400	Weak transcription	Hela-S3	cervix
27	chr5:118453000-118472400	Weak transcription	Psoas Muscle	Psoas
28	chr5:118453400-118465000	Weak transcription	HUVEC	blood vessel
29	chr5:118453600-118465200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:118453600-118471200	Weak transcription	Aorta	Aorta
31	chr5:118453800-118465200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:118453800-118522800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:118454000-118465000	Weak transcription	Fetal Kidney	kidney
34	chr5:118454000-118465000	Weak transcription	HSMMtube	muscle
35	chr5:118454000-118465200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:118454200-118465000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:118454200-118468800	Weak transcription	Osteobl	bone
38	chr5:118454600-118465200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:118454800-118465000	Weak transcription	NH-A	brain
40	chr5:118455000-118465000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:118455000-118465400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:118456000-118465200	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:118456200-118468600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr5:118456800-118465000	Weak transcription	K562	blood
45	chr5:118456800-118465200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:118456800-118469200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:118456800-118483200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:118456800-118484600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:118457000-118464200	Weak transcription	GM12878-XiMat	blood
50	chr5:118457000-118465000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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