Variant report

Variant	rs6446204
Chromosome Location	chr3:49034879-49034880
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	CTCF	chr3:49034781-49034948	HepG2	liver:	n/a	n/a
2	CTCF	chr3:49034628-49035081	K562	blood:	n/a	n/a
3	CTCF	chr3:49034805-49034906	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr3:49034651-49035006	HepG2	liver:	n/a	n/a
5	USF1	chr3:49034705-49034917	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49034618-49034900	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:49034708-49034992	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:49034696-49035020	GM12891	blood:	n/a	n/a
9	CTCF	chr3:49034820-49034970	BE2_C	brain:	n/a	n/a
10	RAD21	chr3:49034768-49034986	HepG2	liver:	n/a	chr3:49034857-49034876 chr3:49034862-49034874 chr3:49034862-49034872 chr3:49034860-49034873
11	POLR2A	chr3:49034845-49035106	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:49034742-49035021	K562	blood:	n/a	n/a
13	CTCF	chr3:49034780-49034930	SK-N-SH_RA	brain:	n/a	n/a
14	POLR2A	chr3:49034661-49034895	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:49034740-49034890	K562	blood:	n/a	n/a
16	CTCF	chr3:49034800-49034950	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr3:49034717-49034983	HepG2	liver:	n/a	n/a
18	CTCF	chr3:49034744-49034955	K562	blood:	n/a	n/a
19	ZNF263	chr3:49034833-49035226	HEK293-T-REx	kidney:	n/a	n/a
20	CTCF	chr3:49034780-49034930	HRPEpiC	eye:	n/a	n/a
21	CTCF	chr3:49034780-49034930	HBMEC	blood vessel:	n/a	n/a
22	CTCF	chr3:49034838-49034899	GM12878	blood:	n/a	n/a
23	RAD21	chr3:49034742-49035002	HepG2	liver:	n/a	chr3:49034860-49034873 chr3:49034862-49034874 chr3:49034857-49034876 chr3:49034862-49034872
24	CTCF	chr3:49034760-49034910	HEK293	kidney:	n/a	n/a
25	CTCF	chr3:49034780-49034930	HepG2	liver:	n/a	n/a
26	CTCF	chr3:49034760-49034910	NB4	blood:	n/a	n/a
27	CTCF	chr3:49034800-49034950	BE2_C	brain:	n/a	n/a
28	CTCF	chr3:49034800-49034950	HPAF	blood vessel:	n/a	n/a
29	CTCF	chr3:49034735-49034969	K562	blood:	n/a	n/a
30	SMC3	chr3:49034787-49034987	HepG2	liver:	n/a	chr3:49034862-49034872
31	CTCF	chr3:49034820-49034970	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr3:49034777-49034949	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
P4HTM	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11130181	0.86[EUR][1000 genomes]
rs11130183	0.82[CEU][hapmap]
rs11707968	0.92[EUR][1000 genomes]
rs12715430	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13099075	0.93[EUR][1000 genomes]
rs3087866	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4292260	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs4955411	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs4955416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4955426	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974083	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];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4974088	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];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62259536	0.85[EUR][1000 genomes]
rs6414614	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446200	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446247	0.91[EUR][1000 genomes]
rs6446256	0.85[CEU][hapmap]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs6787808	1.00[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7100	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7372883	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7429661	0.82[CEU][hapmap]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7621347	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap]
rs9810318	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9834003	0.82[CEU][hapmap]
rs9859473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9865051	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs9879978	1.00[CEU][hapmap]

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs6446204	AMT	cis	Thyroid	GTEx
rs6446204	IQCF1	cis	cerebellum	SCAN
rs6446204	AMT	cis	Whole Blood	GTEx
rs6446204	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6446204	WDR6	cis	cerebellum	SCAN
rs6446204	AMT	cis	Esophagus Mucosa	GTEx
rs6446204	WDR6	cis	Muscle Skeletal	GTEx
rs6446204	NICN1	cis	parietal	SCAN
rs6446204	NICN1-AS1	cis	Thyroid	GTEx
rs6446204	AMT	cis	Nerve Tibial	GTEx
rs6446204	NICN1	cis	Thyroid	GTEx
rs6446204	LZTFL1	cis	cerebellum	SCAN
rs6446204	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6446204	DALRD3	cis	cerebellum	SCAN
rs6446204	NICN1	cis	cerebellum	SCAN
rs6446204	AMT	cis	Artery Aorta	GTEx
rs6446204	PHF7	cis	parietal	SCAN
rs6446204	AMT	cis	Artery Tibial	GTEx
rs6446204	AMT	cis	cerebellum	SCAN
rs6446204	TLR9	cis	parietal	SCAN
rs6446204	NCKIPSD	cis	parietal	SCAN
rs6446204	WDR6	cis	parietal	SCAN
rs6446204	AMT	cis	lung	GTEx
rs6446204	ZNF589	cis	parietal	SCAN
rs6446204	P4HTM	cis	parietal	SCAN
rs6446204	GPX1	cis	parietal	SCAN
rs6446204	AMT	cis	parietal	SCAN
rs6446204	QRICH1	cis	cerebellum	SCAN
rs6446204	DALRD3	cis	parietal	SCAN
rs6446204	AMT	cis	lymphoblastoid	seeQTL
rs6446204	WDR6	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49028400-49035600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:49028800-49043600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:49029000-49043600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49029000-49043800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:49029200-49035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:49029200-49035600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:49029200-49036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:49029200-49043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:49029200-49043400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:49029400-49035400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49029400-49036600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:49029400-49036600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:49029400-49036800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:49029400-49039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:49029400-49041600	Weak transcription	Liver	Liver
16	chr3:49029400-49043400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:49029400-49043600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:49029400-49043600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:49029400-49043600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:49029400-49043600	Weak transcription	NH-A	brain
21	chr3:49029400-49043800	Weak transcription	Psoas Muscle	Psoas
22	chr3:49029400-49043800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:49029600-49036600	Weak transcription	Pancreas	Pancrea
24	chr3:49029600-49039000	Weak transcription	Right Ventricle	heart
25	chr3:49029600-49040200	Weak transcription	Fetal Lung	lung
26	chr3:49029600-49042000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:49029600-49042200	Weak transcription	Ovary	ovary
28	chr3:49029600-49042400	Weak transcription	HMEC	breast
29	chr3:49029600-49043400	Weak transcription	Esophagus	oesophagus
30	chr3:49029600-49043400	Weak transcription	Fetal Kidney	kidney
31	chr3:49029600-49043400	Weak transcription	GM12878-XiMat	blood
32	chr3:49029600-49043400	Weak transcription	NHDF-Ad	bronchial
33	chr3:49029600-49043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49029600-49043600	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:49029600-49043600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:49029600-49043800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:49029600-49043800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:49029600-49043800	Weak transcription	HSMM	muscle
39	chr3:49029600-49043800	Weak transcription	HSMMtube	muscle
40	chr3:49029800-49035000	Weak transcription	Hela-S3	cervix
41	chr3:49029800-49040000	Weak transcription	Stomach Mucosa	stomach
42	chr3:49029800-49043400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:49029800-49043400	Weak transcription	Dnd41	blood
44	chr3:49029800-49043600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:49029800-49043600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:49029800-49043600	Weak transcription	A549	lung
47	chr3:49030000-49043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:49030000-49043800	Weak transcription	Small Intestine	intestine
49	chr3:49030200-49035400	Strong transcription	Fetal Stomach	stomach
50	chr3:49030400-49035800	Strong transcription	Fetal Intestine Small	intestine

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