Variant report

Variant	rs9864243
Chromosome Location	chr3:48982732-48982733
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	chr3:48981034..48982977-chr3:49056933..49058838,2	K562	blood:

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000207605	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 33 )

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

rs_ID	r²[population]
rs11130181	0.82[EUR][1000 genomes]
rs11707968	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12715430	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13099075	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];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[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];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[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];0.82[YRI][hapmap]
rs6796790	0.80[EUR][1000 genomes]
rs6798112	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6801211	0.80[EUR][1000 genomes]
rs7100	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[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];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621347	0.82[EUR][1000 genomes]
rs7639370	0.82[EUR][1000 genomes]
rs7653408	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]
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];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9865051	1.00[ASW][hapmap];0.95[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs9864243	IQCF1	cis	cerebellum	SCAN
rs9864243	PHF7	cis	parietal	SCAN
rs9864243	NICN1	cis	parietal	SCAN
rs9864243	WDR6	cis	parietal	SCAN
rs9864243	NICN1	cis	Thyroid	GTEx
rs9864243	NCKIPSD	cis	parietal	SCAN
rs9864243	WDR6	cis	Muscle Skeletal	GTEx
rs9864243	AMT	cis	parietal	SCAN
rs9864243	AMT	cis	cerebellum	SCAN
rs9864243	QRICH1	cis	cerebellum	SCAN
rs9864243	WDR6	cis	Nerve Tibial	GTEx
rs9864243	NICN1	cis	cerebellum	SCAN
rs9864243	GPX1	cis	parietal	SCAN
rs9864243	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9864243	AMT	cis	Thyroid	GTEx
rs9864243	AMT	cis	Nerve Tibial	GTEx
rs9864243	P4HTM	cis	parietal	SCAN
rs9864243	ZNF589	cis	parietal	SCAN
rs9864243	DALRD3	cis	parietal	SCAN
rs9864243	TLR9	cis	parietal	SCAN
rs9864243	ARIH2	cis	Thyroid	GTEx
rs9864243	AMT	cis	lung	GTEx
rs9864243	WDR6	cis	cerebellum	SCAN
rs9864243	AMT	cis	Artery Tibial	GTEx
rs9864243	NCKIPSD	cis	Nerve Tibial	GTEx
rs9864243	P4HTM	cis	lung	GTEx
rs9864243	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9864243	AMT	cis	Artery Aorta	GTEx
rs9864243	AMT	cis	Adipose Subcutaneous	GTEx
rs9864243	AMT	cis	Whole Blood	GTEx
rs9864243	DALRD3	cis	cerebellum	SCAN
rs9864243	LZTFL1	cis	cerebellum	SCAN
rs9864243	NICN1-AS1	cis	Thyroid	GTEx

Chromatin state (count:122 , 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	chr3:48962000-49000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:48965200-49004200	Weak transcription	Colonic Mucosa	Colon
4	chr3:48965400-49000000	Weak transcription	Esophagus	oesophagus
5	chr3:48965800-48995400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:48965800-49000000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:48965800-49004000	Weak transcription	Fetal Brain Male	brain
8	chr3:48966000-48986000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:48966000-49008000	Weak transcription	Fetal Kidney	kidney
10	chr3:48966600-48986200	Weak transcription	NHLF	lung
11	chr3:48966800-48986200	Weak transcription	HMEC	breast
12	chr3:48967400-48994800	Weak transcription	Gastric	stomach
13	chr3:48967600-48983400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:48968000-48997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:48968200-48997200	Weak transcription	NHDF-Ad	bronchial
16	chr3:48970400-48984000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:48970400-49004400	Weak transcription	Pancreas	Pancrea
18	chr3:48970600-48991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:48970800-48986600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:48970800-48991000	Weak transcription	Lung	lung
21	chr3:48970800-49002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:48971000-48994800	Weak transcription	Spleen	Spleen
23	chr3:48971400-48986200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:48971400-48991000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:48971400-48991000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:48971600-48993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:48972000-49000400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:48972400-48991200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:48972400-48995400	Weak transcription	Brain Germinal Matrix	brain
30	chr3:48972400-48995400	Weak transcription	Ovary	ovary
31	chr3:48972800-48991200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:48973000-48983000	Weak transcription	Fetal Lung	lung
33	chr3:48973400-48983400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:48973400-48986200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:48973400-48986600	Weak transcription	NH-A	brain
36	chr3:48973400-48986800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:48973400-48991400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:48973400-48994800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:48973600-48997600	Weak transcription	Osteobl	bone
40	chr3:48974600-48990400	Weak transcription	Fetal Intestine Small	intestine
41	chr3:48974800-48991400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:48975000-48983400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:48975000-48983600	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:48975000-48991200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:48975000-48999800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:48975200-48991800	Weak transcription	HUVEC	blood vessel
47	chr3:48975400-48990800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:48975800-48983200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:48976000-48987000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:48976200-48983800	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links