Variant report

Variant	rs11752886
Chromosome Location	chr6:166746299-166746300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

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	chr6:166742700-166754624	K562	blood:	n/a	n/a
3	POLR2A	chr6:166746147-166749873	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:166746274-166749904	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:166746206-166754614	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:166745653-166751514	GM12892	blood:	n/a	n/a
7	NFATC1	chr6:166746279-166748938	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:166745484-166754512	GM12892	blood:	n/a	n/a
9	NFATC1	chr6:166746256-166747866	GM12878	blood:	n/a	n/a
10	WRNIP1	chr6:166745983-166747626	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:166745570-166751783	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:166745466-166757224	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:166745668-166754554	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:166746200-166747640	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:166746067-166746336	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr6:166745300-166754633	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:166746202-166746512	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:166746293..166747904-chr6:166796894..166799021,2	K562	blood:
2	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
3	chr6:166745230..166747762-chr6:166754729..166756977,2	MCF-7	breast:

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10455809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455976	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10455977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455978	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946152	0.88[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];0.81[AFR][1000 genomes];0.93[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];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946161	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11551053	0.93[ASN][1000 genomes]
rs11753652	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755305	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209616	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214281	0.89[AFR][1000 genomes];0.93[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];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662920	0.82[EUR][1000 genomes]
rs12662924	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1599841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294333	0.95[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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294335	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[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];1.00[AFR][1000 genomes];0.95[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];0.82[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];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709111	0.82[CHB][hapmap]
rs4710042	0.82[CHB][hapmap]
rs55936781	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59337176	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66461381	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68016351	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6932631	0.95[CEU][hapmap];0.81[AMR][1000 genomes]
rs73030701	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73263155	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73788236	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7740965	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7753161	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767887	0.88[ASN][1000 genomes]
rs7771603	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9347123	0.83[CHB][hapmap]
rs9348119	0.87[CHB][hapmap]
rs9348121	0.82[CHB][hapmap]
rs941683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11752886		cis	Lymphoblastoid	GTEx
rs11752886	SFT2D1	cis	multi-tissue	Pritchard
rs11752886	LOC401284	cis	multi-tissue	Pritchard
rs11752886	LOC135043	cis	multi-tissue	Pritchard
rs11752886	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	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:166739400-166748000	Weak transcription	Gastric	stomach
9	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
11	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:166741400-166750000	Weak transcription	HMEC	breast
14	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:166742600-166746400	Weak transcription	Placenta	Placenta
20	chr6:166742600-166746400	Weak transcription	Lung	lung
21	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
22	chr6:166742800-166746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:166742800-166746400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:166742800-166746400	Weak transcription	Aorta	Aorta
25	chr6:166742800-166746400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:166742800-166746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:166742800-166746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:166742800-166747000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:166742800-166748400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:166742800-166749200	Weak transcription	NHEK	skin
31	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
32	chr6:166742800-166751000	Weak transcription	HSMM	muscle
33	chr6:166743000-166746400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:166743000-166746400	Weak transcription	Thymus	Thymus
35	chr6:166743000-166746800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:166743000-166746800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:166743000-166748000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:166743000-166749200	Weak transcription	Fetal Lung	lung
39	chr6:166743000-166749600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:166743400-166747200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:166743400-166748200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:166743400-166749600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:166743600-166747000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr6:166743800-166746600	Enhancers	Brain Anterior Caudate	brain
45	chr6:166743800-166747200	Enhancers	Brain Cingulate Gyrus	brain
46	chr6:166743800-166747600	Enhancers	Brain Substantia Nigra	brain
47	chr6:166744000-166746400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:166744000-166747200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr6:166744000-166747400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
50	chr6:166744000-166747400	Enhancers	K562	blood

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