Variant report

Variant	rs12214812
Chromosome Location	chr6:166743160-166743161
allele	A/G
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	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:166742537..166744079-chr6:166803763..166806576,2	K562	blood:
2	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
3	chr6:166689019..166690684-chr6:166742246..166744543,2	K562	blood:
4	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:

Variant related genes	Relation type
SFT2D1	TF binding region
HNRNPA1P49	TF binding region
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10455809	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455976	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10455977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455978	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946152	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10946158	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946160	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946161	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11551053	0.93[ASN][1000 genomes]
rs11752886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753652	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755305	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12198613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209616	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214281	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662920	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12662924	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1599841	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294333	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294334	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294335	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709111	0.82[CHB][hapmap]
rs4710042	0.82[CHB][hapmap]
rs55936781	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59337176	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66461381	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68016351	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6932631	0.95[CEU][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs6938819	0.84[AMR][1000 genomes]
rs73030701	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73263155	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73788236	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7740965	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7753161	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767887	0.88[ASN][1000 genomes]
rs7771603	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9347123	0.83[CHB][hapmap]
rs9348115	0.84[AMR][1000 genomes]
rs9348116	0.81[AMR][1000 genomes]
rs9348119	0.87[CHB][hapmap]
rs9348121	0.82[CHB][hapmap]
rs941683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999234	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12214812		cis	Lymphoblastoid	GTEx
rs12214812	LOC135043	cis	multi-tissue	Pritchard
rs12214812	LOC401284	cis	multi-tissue	Pritchard
rs12214812	SFT2D1	cis	lymphoblastoid	seeQTL
rs12214812	SFT2D1	cis	multi-tissue	Pritchard
rs12214812	PRR18	cis	lymphoblastoid	seeQTL
rs12214812	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
2	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
4	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
5	chr6:166730400-166744200	Weak transcription	Fetal Brain Male	brain
6	chr6:166731800-166743400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:166732400-166744000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:166732600-166743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:166732800-166743200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:166733200-166744400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
14	chr6:166733400-166743400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:166733600-166743400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
17	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
18	chr6:166734400-166743200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
20	chr6:166737000-166745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:166737200-166743400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:166738200-166754200	Weak transcription	NH-A	brain
23	chr6:166739400-166744400	Weak transcription	Brain Angular Gyrus	brain
24	chr6:166739400-166745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:166739400-166748000	Weak transcription	Gastric	stomach
27	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:166739600-166743400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:166739600-166743400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:166739800-166743800	Weak transcription	NHLF	lung
31	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
32	chr6:166740200-166743800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:166740200-166744000	Weak transcription	Right Ventricle	heart
34	chr6:166740200-166744200	Weak transcription	A549	lung
35	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
36	chr6:166740800-166744000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:166741000-166744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:166741400-166743800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:166741400-166744200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:166741400-166744200	Weak transcription	Esophagus	oesophagus
41	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:166741400-166750000	Weak transcription	HMEC	breast
43	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:166741600-166744200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:166742200-166743600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:166742200-166744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:166742400-166744000	Weak transcription	Muscle Satellite Cultured Cells	--

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