Variant report

Variant	rs12939138
Chromosome Location	chr17:33901578-33901579
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	chr17:33901519-33901773	K562	blood:	n/a	n/a
2	POLR2A	chr17:33901409-33907583	K562	blood:	n/a	n/a
3	POLR2A	chr17:33901538-33907315	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33893761..33897248-chr17:33899377..33902990,5	MCF-7	breast:

Variant related genes	Relation type
AP2B1	TF binding region
ENSG00000267321	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11650225	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650621	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651380	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652390	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653354	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654542	1.00[ASN][1000 genomes]
rs11655098	1.00[YRI][hapmap]
rs11656872	0.84[ASW][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657558	1.00[ASN][1000 genomes]
rs12936539	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936693	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12937370	0.81[AFR][1000 genomes]
rs12939481	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939818	0.81[AFR][1000 genomes]
rs12940370	0.81[AFR][1000 genomes]
rs12940422	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940584	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941376	1.00[YRI][hapmap]
rs12943224	1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945102	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945419	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12945980	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12947274	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949877	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951703	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17606150	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608253	1.00[ASN][1000 genomes]
rs17638076	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669281	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670584	1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670614	0.81[EUR][1000 genomes]
rs17676508	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34063751	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34874930	1.00[ASN][1000 genomes]
rs34937989	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3506	1.00[ASW][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515868	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672532	1.00[ASN][1000 genomes]
rs35774966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531775	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61752107	0.90[AFR][1000 genomes]
rs71381460	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381461	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381463	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71381465	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381467	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381469	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12939138	VWDE	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33895800-33904200	Weak transcription	Right Atrium	heart
2	chr17:33895800-33904800	Weak transcription	Ovary	ovary
3	chr17:33896000-33902200	Weak transcription	HSMMtube	muscle
4	chr17:33896000-33903800	Weak transcription	Brain Angular Gyrus	brain
5	chr17:33896000-33904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:33896200-33905000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:33896200-33905000	Weak transcription	Aorta	Aorta
8	chr17:33896400-33901600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:33896400-33902000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr17:33896400-33904000	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:33896400-33904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:33896400-33904200	Weak transcription	Psoas Muscle	Psoas
13	chr17:33896400-33904600	Weak transcription	Stomach Mucosa	stomach
14	chr17:33896400-33904800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:33896400-33904800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:33896400-33904800	Weak transcription	Colonic Mucosa	Colon
17	chr17:33896400-33904800	Weak transcription	Esophagus	oesophagus
18	chr17:33896400-33904800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:33896400-33904800	Weak transcription	Right Ventricle	heart
20	chr17:33896400-33905000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:33896400-33905000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:33896600-33904400	Weak transcription	Brain Substantia Nigra	brain
23	chr17:33896800-33902400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:33896800-33903600	Weak transcription	NH-A	brain
25	chr17:33896800-33904000	Weak transcription	Pancreas	Pancrea
26	chr17:33896800-33904000	Weak transcription	Osteobl	bone
27	chr17:33896800-33904200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:33897000-33902000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr17:33897000-33902800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:33897000-33904400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:33897400-33902000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr17:33897400-33902000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr17:33897400-33902000	Weak transcription	HMEC	breast
34	chr17:33897400-33904000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:33897600-33901600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:33897600-33901600	Weak transcription	Adipose Nuclei	Adipose
37	chr17:33897600-33901600	Weak transcription	NHDF-Ad	bronchial
38	chr17:33897600-33902000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:33897600-33902000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr17:33897600-33902000	Weak transcription	NHLF	lung
41	chr17:33897600-33902200	Weak transcription	Fetal Brain Female	brain
42	chr17:33897600-33902600	Weak transcription	Brain Anterior Caudate	brain
43	chr17:33897600-33902800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:33897600-33902800	Weak transcription	Brain Hippocampus Middle	brain
45	chr17:33897600-33904400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr17:33897600-33904400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:33897600-33904400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:33897600-33904400	Weak transcription	Fetal Brain Male	brain
49	chr17:33897600-33904400	Weak transcription	HUVEC	blood vessel
50	chr17:33897600-33904600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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