Variant report

Variant	rs2952155
Chromosome Location	chr17:37861718-37861719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr17:37861365-37862697	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr17:37861702-37861740	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37861008..37863729-chr17:37884662..37888113,4	MCF-7	breast:
2	chr17:37859950..37863403-chr17:37895808..37898808,3	MCF-7	breast:
3	chr17:37860742..37863626-chr17:37884816..37888176,3	MCF-7	breast:
4	chr17:37860215..37862693-chr17:37863560..37866176,3	K562	blood:
5	chr17:37855173..37857494-chr17:37859476..37862807,3	K562	blood:
6	chr17:37854371..37858847-chr17:37859204..37863861,12	MCF-7	breast:
7	chr17:37860257..37864274-chr17:37871854..37875164,5	MCF-7	breast:
8	chr17:37842383..37849519-chr17:37854521..37862509,17	MCF-7	breast:
9	chr17:37860636..37865251-chr17:37890921..37895460,5	MCF-7	breast:

No data

Variant related genes	Relation type
ERBB2	TF binding region
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000141738	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1058808	0.96[ASN][1000 genomes]
rs11653998	0.97[ASN][1000 genomes]
rs12150298	0.87[CHB][hapmap]
rs12150603	0.87[CHB][hapmap]
rs12940986	0.87[CHB][hapmap]
rs14050	0.83[CHB][hapmap]
rs1476278	0.87[CHB][hapmap]
rs1565922	0.87[CHB][hapmap]
rs1565923	0.99[ASN][1000 genomes]
rs1810132	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2088126	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2247862	0.83[CHB][hapmap]
rs2313171	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2517951	0.97[ASN][1000 genomes]
rs2517954	0.96[CHB][hapmap]
rs2517955	0.95[CHB][hapmap]
rs2517956	0.95[CHB][hapmap]
rs2517957	0.87[CHB][hapmap]
rs2517958	0.83[CHB][hapmap]
rs2643194	0.97[ASN][1000 genomes]
rs2643195	0.97[ASN][1000 genomes]
rs2904766	0.83[ASN][1000 genomes]
rs2934953	0.83[CHB][hapmap]
rs2934967	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2934971	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2941503	0.83[CHB][hapmap]
rs2941504	0.83[CHB][hapmap]
rs2941505	0.88[CHB][hapmap]
rs2941506	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2952151	0.83[CHB][hapmap]
rs2952156	0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs2952157	0.97[ASN][1000 genomes]
rs4252627	0.98[ASN][1000 genomes]
rs4795393	0.81[ASN][1000 genomes]
rs8078228	0.86[CHB][hapmap]
rs903501	0.87[CHB][hapmap]
rs903502	0.83[CHB][hapmap]
rs903506	0.97[ASN][1000 genomes]
rs907087	0.83[CHB][hapmap]
rs907089	0.87[CHB][hapmap]
rs9303274	0.87[CHB][hapmap]
rs9675194	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2952155	PGAP3	cis	Thyroid	GTEx
rs2952155	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2952155	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37857000-37872000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:37857600-37863400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr17:37857800-37863200	Enhancers	Left Ventricle	heart
4	chr17:37858000-37862200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:37858000-37862400	Genic enhancers	Fetal Stomach	stomach
6	chr17:37858000-37862800	Genic enhancers	Fetal Intestine Large	intestine
7	chr17:37858000-37863200	Weak transcription	HUVEC	blood vessel
8	chr17:37858000-37885200	Weak transcription	Fetal Brain Male	brain
9	chr17:37858000-37885600	Weak transcription	Hela-S3	cervix
10	chr17:37858200-37861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:37858200-37862200	Enhancers	Lung	lung
12	chr17:37858200-37862400	Enhancers	Fetal Lung	lung
13	chr17:37858200-37862400	Enhancers	Gastric	stomach
14	chr17:37858200-37862400	Enhancers	Pancreas	Pancrea
15	chr17:37858200-37863200	Weak transcription	Spleen	Spleen
16	chr17:37858200-37863200	Weak transcription	NHLF	lung
17	chr17:37858200-37863600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:37858200-37864000	Enhancers	Liver	Liver
19	chr17:37858200-37864400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:37858200-37882600	Weak transcription	NHDF-Ad	bronchial
21	chr17:37858400-37862400	Enhancers	Duodenum Mucosa	Duodenum
22	chr17:37858400-37863000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr17:37858400-37863400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:37858400-37863400	Weak transcription	Fetal Kidney	kidney
25	chr17:37858400-37863600	Genic enhancers	Fetal Intestine Small	intestine
26	chr17:37858400-37879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr17:37858600-37861800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:37858600-37861800	Weak transcription	HSMM	muscle
29	chr17:37858800-37862200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:37858800-37862800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:37859000-37862000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:37859000-37863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:37859000-37864000	Genic enhancers	Fetal Muscle Leg	muscle
34	chr17:37859200-37862200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr17:37859200-37863000	Enhancers	Right Ventricle	heart
36	chr17:37859400-37881000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr17:37859600-37861800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr17:37859600-37863600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:37859800-37862200	Enhancers	Placenta	Placenta
40	chr17:37859800-37864800	Weak transcription	Fetal Brain Female	brain
41	chr17:37860200-37862200	Enhancers	HepG2	liver
42	chr17:37860200-37862800	Enhancers	Stomach Smooth Muscle	stomach
43	chr17:37860200-37863000	Enhancers	Stomach Mucosa	stomach
44	chr17:37860400-37862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:37860400-37862600	Enhancers	A549	lung
46	chr17:37860600-37862000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:37860600-37862200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr17:37860600-37862600	Enhancers	HSMMtube	muscle
49	chr17:37860800-37861800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr17:37860800-37862000	Enhancers	Duodenum Smooth Muscle	Duodenum

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