Variant report

Variant	rs4955416
Chromosome Location	chr3:49108428-49108429
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	chr3:49108275..49110303-chr3:49112148..49114668,2	K562	blood:
2	chr3:49067450..49069874-chr3:49105027..49108466,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10154992	0.81[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs11130181	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130183	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[YRI][hapmap]
rs11130186	0.81[ASW][hapmap]
rs1134591	0.82[YRI][hapmap]
rs11707968	0.81[EUR][1000 genomes]
rs13099075	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3087866	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs3212	0.86[YRI][hapmap]
rs4292260	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4521268	0.82[YRI][hapmap]
rs4955411	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4955417	0.86[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs4955421	0.85[YRI][hapmap]
rs4955426	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs4955439	0.82[CEU][hapmap]
rs4955443	0.86[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs4974080	0.86[YRI][hapmap]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4974085	0.82[YRI][hapmap]
rs4974087	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs6414614	0.88[EUR][1000 genomes]
rs6446196	0.81[ASW][hapmap];0.86[YRI][hapmap]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6446205	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6446247	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446252	0.92[YRI][hapmap]
rs6446253	0.84[YRI][hapmap]
rs6446256	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs6446257	0.81[CEU][hapmap]
rs6769821	0.82[CEU][hapmap]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6779394	0.81[ASW][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs6781790	0.82[YRI][hapmap]
rs6787808	1.00[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7100	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs7373790	0.90[AFR][1000 genomes]
rs7429661	0.82[CEU][hapmap]
rs7430198	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs7432989	0.81[ASW][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7617480	0.93[ASW][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7619016	0.86[CEU][hapmap]
rs7619073	0.80[EUR][1000 genomes]
rs7621015	0.82[YRI][hapmap]
rs7621226	1.00[CEU][hapmap]
rs7621347	0.96[EUR][1000 genomes]
rs7626076	0.86[CEU][hapmap]
rs7626445	0.82[YRI][hapmap]
rs7643368	0.82[YRI][hapmap]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9586	0.87[ASW][hapmap];0.86[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9637481	0.89[YRI][hapmap]
rs9810318	0.89[EUR][1000 genomes]
rs9831648	0.87[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9834003	0.81[ASW][hapmap];0.82[CEU][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap]
rs9840050	0.86[YRI][hapmap]
rs9846123	0.82[YRI][hapmap]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9865051	0.95[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9884022	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs4955416	QRICH1	cis	cerebellum	SCAN
rs4955416	AMT	cis	Thyroid	GTEx
rs4955416	QRICH1	cis	Nerve Tibial	GTEx
rs4955416	TLR9	cis	parietal	SCAN
rs4955416	AMT	cis	Artery Tibial	GTEx
rs4955416	NICN1-AS1	cis	Thyroid	GTEx
rs4955416	P4HTM	cis	parietal	SCAN
rs4955416	ZNF589	cis	parietal	SCAN
rs4955416	AMT	cis	lung	GTEx
rs4955416	LZTFL1	cis	cerebellum	SCAN
rs4955416	WDR6	cis	cerebellum	SCAN
rs4955416	WDR6	cis	parietal	SCAN
rs4955416	GPX1	cis	parietal	SCAN
rs4955416	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4955416	DALRD3	cis	cerebellum	SCAN
rs4955416	NICN1	cis	parietal	SCAN
rs4955416	AMT	cis	cerebellum	SCAN
rs4955416	NCKIPSD	cis	Nerve Tibial	GTEx
rs4955416	DALRD3	cis	parietal	SCAN
rs4955416	AMT	cis	Nerve Tibial	GTEx
rs4955416	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4955416	IQCF1	cis	cerebellum	SCAN
rs4955416	NICN1	cis	Thyroid	GTEx
rs4955416	WDR6	cis	Nerve Tibial	GTEx
rs4955416	PHF7	cis	parietal	SCAN
rs4955416	NICN1	cis	cerebellum	SCAN
rs4955416	AMT	cis	Whole Blood	GTEx
rs4955416	WDR6	cis	Muscle Skeletal	GTEx
rs4955416	AMT	cis	Adipose Subcutaneous	GTEx
rs4955416	NCKIPSD	cis	parietal	SCAN
rs4955416	AMT	cis	lymphoblastoid	seeQTL
rs4955416	WDR6	cis	Heart Left Ventricle	GTEx
rs4955416	WDR6	cis	lung	GTEx
rs4955416	AMT	cis	parietal	SCAN
rs4955416	PH-4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
4	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
7	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
8	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
9	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
12	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:49073400-49118200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:49077400-49117200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:49084600-49110800	Weak transcription	Fetal Heart	heart
18	chr3:49084600-49117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49087800-49115200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49087800-49117600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:49088000-49115400	Strong transcription	Liver	Liver
22	chr3:49088000-49116800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:49088000-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:49088000-49118400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49088200-49116800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:49088400-49116800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:49088600-49116400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:49088600-49116800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:49088600-49116800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:49094600-49128200	Weak transcription	Fetal Brain Male	brain
31	chr3:49094800-49113400	Weak transcription	Psoas Muscle	Psoas
32	chr3:49095000-49117000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:49095200-49109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:49095200-49117200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:49095400-49129600	Weak transcription	Stomach Mucosa	stomach
36	chr3:49096400-49116800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:49096800-49116800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:49096800-49116800	Strong transcription	Placenta	Placenta
39	chr3:49096800-49117200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:49097200-49117200	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:49097800-49118200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:49097800-49118200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:49098000-49114200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:49098000-49114800	Strong transcription	Fetal Intestine Large	intestine
45	chr3:49098000-49115200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:49098000-49115200	Strong transcription	Fetal Brain Female	brain
47	chr3:49098000-49115600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:49098000-49116000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:49098000-49116800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:49098000-49116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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