Variant report

Variant	rs7653408
Chromosome Location	chr3:48972351-48972352
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48954704..48957536-chr3:48971085..48974504,3	K562	blood:
2	chr3:48970141..48972783-chr3:48973046..48975012,2	K562	blood:
3	chr3:48955916..48957536-chr3:48971693..48973834,2	K562	blood:
4	chr3:48963303..48970109-chr3:48970555..48975034,7	K562	blood:
5	chr3:48971937..48973557-chr3:48975167..48976698,2	K562	blood:

Variant related genes	Relation type
ENSG00000177479	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 36 )

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

rs_ID	r²[population]
rs11130181	0.82[EUR][1000 genomes]
rs11707968	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12715430	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13099075	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs3087866	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4292260	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4955411	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4955416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4955426	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4974081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs62259536	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6414614	0.88[EUR][1000 genomes]
rs6446200	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446247	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6766238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6787808	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6796790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs6798112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7100	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7372883	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7429596	0.81[EUR][1000 genomes]
rs7434187	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621347	0.82[EUR][1000 genomes]
rs7639370	0.82[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9810318	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9859473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9864243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9865051	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs7653408	WDR6	cis	parietal	SCAN
rs7653408	DALRD3	cis	parietal	SCAN
rs7653408	ARIH2	cis	Thyroid	GTEx
rs7653408	ZNF589	cis	parietal	SCAN
rs7653408	AMT	cis	multi-tissue	Pritchard
rs7653408	NCKIPSD	cis	multi-tissue	Pritchard
rs7653408	AMT	cis	Artery Tibial	GTEx
rs7653408	NCKIPSD	cis	parietal	SCAN
rs7653408	LZTFL1	cis	cerebellum	SCAN
rs7653408	P4HTM	cis	lung	GTEx
rs7653408	DALRD3	cis	cerebellum	SCAN
rs7653408	AMT	cis	Whole Blood	GTEx
rs7653408	AMT	cis	parietal	SCAN
rs7653408	WDR6	cis	multi-tissue	Pritchard
rs7653408	AMT	cis	lymphoblastoid	seeQTL
rs7653408	NICN1	cis	parietal	SCAN
rs7653408	WDR6	cis	Nerve Tibial	GTEx
rs7653408	NICN1-AS1	cis	Thyroid	GTEx
rs7653408	AMT	cis	Thyroid	GTEx
rs7653408	WDR6	cis	cerebellum	SCAN
rs7653408	PHF7	cis	parietal	SCAN
rs7653408	NICN1	cis	multi-tissue	Pritchard
rs7653408	AMT	cis	Adipose Subcutaneous	GTEx
rs7653408	AMT	cis	Nerve Tibial	GTEx
rs7653408	AMT	cis	Artery Aorta	GTEx
rs7653408	QRICH1	cis	cerebellum	SCAN
rs7653408	AMT	cis	cerebellum	SCAN
rs7653408	NICN1	cis	Thyroid	GTEx
rs7653408	NICN1	cis	cerebellum	SCAN
rs7653408	P4HTM	cis	parietal	SCAN
rs7653408	TLR9	cis	parietal	SCAN
rs7653408	IQCF1	cis	cerebellum	SCAN
rs7653408	GPX1	cis	parietal	SCAN
rs7653408	AMT	cis	lung	GTEx
rs7653408	WDR6	cis	Muscle Skeletal	GTEx
rs7653408	NCKIPSD	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48957600-48974400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48959000-48974000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:48959000-48976000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:48959000-48976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:48959200-48973600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:48959400-48976200	Strong transcription	Fetal Thymus	thymus
8	chr3:48959600-48975800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:48962000-49000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:48965200-49004200	Weak transcription	Colonic Mucosa	Colon
11	chr3:48965400-48981200	Weak transcription	Right Ventricle	heart
12	chr3:48965400-49000000	Weak transcription	Esophagus	oesophagus
13	chr3:48965600-48973800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:48965800-48995400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:48965800-49000000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:48965800-49004000	Weak transcription	Fetal Brain Male	brain
17	chr3:48966000-48973600	Strong transcription	Dnd41	blood
18	chr3:48966000-48986000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:48966000-49008000	Weak transcription	Fetal Kidney	kidney
20	chr3:48966400-48975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:48966600-48972600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:48966600-48986200	Weak transcription	NHLF	lung
23	chr3:48966800-48986200	Weak transcription	HMEC	breast
24	chr3:48967200-48972800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:48967200-48977200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:48967200-48980800	Weak transcription	Aorta	Aorta
27	chr3:48967400-48972800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:48967400-48973400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:48967400-48994800	Weak transcription	Gastric	stomach
30	chr3:48967600-48983400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:48968000-48997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:48968200-48972400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:48968200-48973000	Weak transcription	Stomach Mucosa	stomach
34	chr3:48968200-48976200	Weak transcription	Small Intestine	intestine
35	chr3:48968200-48997200	Weak transcription	NHDF-Ad	bronchial
36	chr3:48969400-48972800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:48969400-48973600	Strong transcription	Fetal Intestine Large	intestine
38	chr3:48969400-48975000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:48969600-48973400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:48969600-48973400	Strong transcription	Placenta	Placenta
41	chr3:48969600-48973600	Strong transcription	Primary T cells from cord blood	blood
42	chr3:48969600-48973800	Strong transcription	NHEK	skin
43	chr3:48969800-48972600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:48969800-48974000	Strong transcription	Hela-S3	cervix
45	chr3:48970000-48972400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:48970000-48972400	Strong transcription	Thymus	Thymus
47	chr3:48970000-48973400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:48970200-48972800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:48970200-48973000	Strong transcription	Fetal Lung	lung
50	chr3:48970200-48973600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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