Variant report

Variant	rs12198613
Chromosome Location	chr6:166747907-166747908
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	POLR2A	chr6:166746252-166749844	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:166747895-166748701	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:166746318-166748671	HL-60	blood:	n/a	n/a
4	POLR2A	chr6:166747027-166748876	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:166746571-166749863	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:166747624-166748161	HepG2	liver:	n/a	n/a
7	STAT5A	chr6:166746423-166747957	GM12878	blood:	n/a	chr6:166746641-166746652 chr6:166747288-166747300
8	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a
9	POLR2A	chr6:166746147-166749873	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:166746274-166749904	GM12891	blood:	n/a	n/a
11	POLR2A	chr6:166747740-166748058	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:166746606-166748421	GM19193	blood:	n/a	n/a
13	POLR2A	chr6:166746206-166754614	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:166745653-166751514	GM12892	blood:	n/a	n/a
15	NFATC1	chr6:166746279-166748938	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:166745484-166754512	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:166747886-166748929	K562	blood:	n/a	n/a
18	POLR2A	chr6:166745570-166751783	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:166747421-166748641	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:166746608-166747921	HL-60	blood:	n/a	n/a
21	POLR2A	chr6:166746365-166757465	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:166747865-166748849	K562	blood:	n/a	n/a
23	POLR2A	chr6:166745466-166757224	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:166747739-166748100	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:166745668-166754554	GM12878	blood:	n/a	n/a
26	PML	chr6:166746746-166748099	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:166747539-166748890	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:166745300-166754633	GM12891	blood:	n/a	n/a
29	MTA3	chr6:166746591-166750124	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:166747648-166748914	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10455809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.86[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];0.97[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];1.00[JPT][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]
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]
rs12214812	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]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[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[JPT][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[JPT][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	1.00[CEU][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	0.96[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:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12198613	LOC401284	cis	multi-tissue	Pritchard
rs12198613	LOC135043	cis	multi-tissue	Pritchard
rs12198613	SFT2D1	cis	multi-tissue	Pritchard
rs12198613		cis	Lymphoblastoid	GTEx
rs12198613	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
3	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
4	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
5	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
6	chr6:166738200-166754200	Weak transcription	NH-A	brain
7	chr6:166739400-166748000	Weak transcription	Gastric	stomach
8	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
10	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
11	chr6:166741400-166750000	Weak transcription	HMEC	breast
12	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
16	chr6:166742800-166748400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:166742800-166749200	Weak transcription	NHEK	skin
18	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
19	chr6:166742800-166751000	Weak transcription	HSMM	muscle
20	chr6:166743000-166748000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:166743000-166749200	Weak transcription	Fetal Lung	lung
22	chr6:166743000-166749600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:166743400-166748200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:166743400-166749600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:166744400-166750600	Weak transcription	NHLF	lung
26	chr6:166744400-166752000	Weak transcription	Right Atrium	heart
27	chr6:166744400-166754800	Weak transcription	NHDF-Ad	bronchial
28	chr6:166744600-166748200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:166744600-166748200	Weak transcription	Liver	Liver
30	chr6:166744600-166748400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:166744600-166750400	Weak transcription	Ovary	ovary
32	chr6:166744800-166749400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:166745000-166748000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:166745200-166749400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:166745200-166750400	Weak transcription	Stomach Mucosa	stomach
36	chr6:166745400-166748000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:166745400-166748000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:166745400-166754400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:166745400-166755000	Weak transcription	A549	lung
40	chr6:166745600-166748200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:166745600-166749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:166745600-166749200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:166745800-166748000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:166745800-166748800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:166745800-166749200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:166745800-166749800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:166745800-166752200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:166746000-166752000	Strong transcription	Fetal Intestine Large	intestine
49	chr6:166746200-166748200	Genic enhancers	Primary B cells from cord blood	blood
50	chr6:166746200-166748200	Genic enhancers	Adipose Nuclei	Adipose

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