Variant report

Variant	rs2934971
Chromosome Location	chr17:37854507-37854508
allele	G/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	NR2F2	chr17:37854293-37854530	K562	blood:	n/a	n/a
2	TEAD4	chr17:37854300-37854573	K562	blood:	n/a	n/a
3	GATA2	chr17:37854303-37854620	K562	blood:	n/a	n/a
4	EP300	chr17:37854465-37854555	K562	blood:	n/a	n/a
5	TAL1	chr17:37854293-37854625	K562	blood:	n/a	n/a
6	ZNF384	chr17:37854345-37854574	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37854371..37858847-chr17:37859204..37863861,12	MCF-7	breast:
2	chr17:37852050..37854882-chr17:37862447..37865325,2	K562	blood:

Variant related genes	Relation type
PGAP3	TF binding region
ERBB2	TF binding region
ENSG00000141736	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1058808	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11653998	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150298	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs12150603	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs12940986	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs14050	0.90[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs1476278	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs1565922	0.87[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1565923	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810132	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088126	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247862	0.90[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2271308	0.80[CHD][hapmap]
rs2313171	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2517951	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517954	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs2517955	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2517956	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs2517957	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2517958	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2517959	0.83[AMR][1000 genomes]
rs2643194	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2643195	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904766	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2934952	0.94[CEU][hapmap]
rs2934953	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs2934967	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941503	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs2941504	0.90[CEU][hapmap];0.83[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2941505	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2941506	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2941520	0.85[EUR][1000 genomes]
rs2952151	0.90[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs2952155	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2952156	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952157	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4252627	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795393	0.80[ASN][1000 genomes]
rs8078228	0.80[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs903501	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs903502	0.81[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs903506	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907087	0.94[ASW][hapmap];0.90[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap]
rs907089	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs9303274	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs931992	0.80[CHD][hapmap]
rs9675194	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs9972882	0.83[GIH][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2934971	MED24	cis	parietal	SCAN
rs2934971	GSDMB	cis	cerebellum	SCAN
rs2934971	DHRS11	cis	cerebellum	SCAN
rs2934971	PGAP3	cis	Thyroid	GTEx
rs2934971	PNMT	cis	parietal	SCAN
rs2934971	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2934971	ORMDL3	cis	lymphoblastoid	seeQTL
rs2934971	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2934971	SLFN14	cis	parietal	SCAN
rs2934971	PGAP3	cis	cerebellum	SCAN
rs2934971	PGAP3	cis	Heart Left Ventricle	GTEx
rs2934971	SPACA3	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37845000-37856000	Weak transcription	Lung	lung
2	chr17:37845200-37854600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:37845200-37854600	Weak transcription	Brain Hippocampus Middle	brain
4	chr17:37845400-37854800	Weak transcription	Placenta	Placenta
5	chr17:37845400-37855000	Weak transcription	Brain Substantia Nigra	brain
6	chr17:37845400-37855400	Weak transcription	Left Ventricle	heart
7	chr17:37845400-37855800	Weak transcription	Aorta	Aorta
8	chr17:37845600-37854600	Weak transcription	Primary B cells from cord blood	blood
9	chr17:37845600-37855000	Weak transcription	Fetal Brain Female	brain
10	chr17:37845600-37855400	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:37845600-37855800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr17:37845600-37855800	Weak transcription	Ovary	ovary
13	chr17:37845600-37855800	Weak transcription	Psoas Muscle	Psoas
14	chr17:37845600-37855800	Weak transcription	Right Ventricle	heart
15	chr17:37845600-37855800	Weak transcription	HSMMtube	muscle
16	chr17:37845600-37856000	Weak transcription	Esophagus	oesophagus
17	chr17:37845600-37856000	Weak transcription	Spleen	Spleen
18	chr17:37845800-37854800	Weak transcription	Primary T cells from cord blood	blood
19	chr17:37845800-37854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:37845800-37855600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:37845800-37855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:37845800-37855600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:37845800-37855600	Weak transcription	NHEK	skin
24	chr17:37845800-37855800	Weak transcription	HSMM	muscle
25	chr17:37845800-37855800	Weak transcription	NHLF	lung
26	chr17:37845800-37858000	Weak transcription	K562	blood
27	chr17:37851600-37855600	Weak transcription	Fetal Stomach	stomach
28	chr17:37851800-37855600	Weak transcription	Fetal Lung	lung
29	chr17:37852000-37854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:37852000-37855800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:37852000-37855800	Weak transcription	Brain Anterior Caudate	brain
32	chr17:37852200-37855600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr17:37852200-37855800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr17:37852200-37856000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:37852400-37855200	Weak transcription	Fetal Muscle Leg	muscle
36	chr17:37852400-37855600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr17:37852400-37855800	Weak transcription	Colonic Mucosa	Colon
38	chr17:37852400-37855800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:37852600-37855600	Weak transcription	Stomach Mucosa	stomach
40	chr17:37852600-37855800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr17:37852800-37855200	Weak transcription	Fetal Heart	heart
42	chr17:37852800-37855400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr17:37852800-37855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:37853000-37854800	Weak transcription	Fetal Intestine Large	intestine
45	chr17:37853000-37855200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:37853000-37855400	Weak transcription	Liver	Liver
47	chr17:37853000-37855600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:37853000-37855600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:37853000-37855800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:37853000-37855800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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