Variant report

Variant	rs7556304
Chromosome Location	chr1:155139509-155139510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155138893..155143080-chr1:155146950..155151161,7	MCF-7	breast:
2	chr1:155053391..155061594-chr1:155138130..155142281,13	MCF-7	breast:
3	chr1:155132887..155135800-chr1:155138561..155141355,2	K562	blood:
4	chr1:155052864..155055747-chr1:155138816..155141443,2	K562	blood:
5	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
6	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
7	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
8	chr1:155139118..155143025-chr1:155155964..155158470,4	MCF-7	breast:
9	chr1:155131530..155134967-chr1:155138392..155140574,4	MCF-7	breast:
10	chr1:155063589..155064900-chr1:155139461..155140960,10	MCF-7	breast:
11	chr1:155110780..155114663-chr1:155139164..155142857,6	MCF-7	breast:
12	chr1:155138080..155140113-chr1:155163279..155166222,2	K562	blood:
13	chr1:155096142..155099007-chr1:155138958..155141461,2	K562	blood:
14	chr1:155106324..155115462-chr1:155131611..155142074,22	MCF-7	breast:
15	chr1:155028322..155031856-chr1:155138984..155141470,4	MCF-7	breast:
16	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
17	chr1:154972832..154975492-chr1:155138295..155140092,2	MCF-7	breast:
18	chr1:155022834..155025487-chr1:155138702..155140475,2	MCF-7	breast:
19	chr1:155131988..155135383-chr1:155138366..155142220,5	MCF-7	breast:
20	chr1:155139047..155141231-chr1:155177826..155180456,2	K562	blood:
21	chr1:155034849..155038242-chr1:155138708..155141835,3	K562	blood:
22	chr1:155074516..155076079-chr1:155138849..155141341,2	MCF-7	breast:
23	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160685	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000271748	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10157801	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs10908458	1.00[CHB][hapmap]
rs11264337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799962	0.82[ASN][1000 genomes]
rs12025371	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12028043	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs12127609	0.82[ASN][1000 genomes]
rs12411216	0.83[ASN][1000 genomes]
rs12752585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs2066981	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs2075570	0.82[ASN][1000 genomes]
rs2075571	0.82[JPT][hapmap]
rs28445596	0.81[ASN][1000 genomes]
rs2974935	0.83[ASN][1000 genomes]
rs2974937	0.83[ASN][1000 genomes]
rs2990220	0.80[ASN][1000 genomes]
rs3814316	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs4072037	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs4246529	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4276913	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4276914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4421576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4460629	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4971052	0.90[CHB][hapmap]
rs4971059	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4971066	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4971073	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs4971076	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs4971079	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971093	0.80[ASN][1000 genomes]
rs4971100	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs6665822	0.80[GIH][hapmap]
rs6676150	0.93[AFR][1000 genomes]
rs7364524	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs760077	0.80[ASN][1000 genomes]
rs914615	0.84[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs9297	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs9426886	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7556304	CRNN	cis	cerebellum	SCAN
rs7556304	GBAP1	cis	Artery Tibial	GTEx
rs7556304	THEM5	cis	parietal	SCAN
rs7556304	S100A7L2	cis	parietal	SCAN
rs7556304	GBAP1	cis	Thyroid	GTEx
rs7556304	IVL	cis	parietal	SCAN
rs7556304	GBAP1	cis	lung	GTEx
rs7556304	PRUNE	cis	cerebellum	SCAN
rs7556304	THBS3	cis	Whole Blood	GTEx
rs7556304	RPRD2	cis	parietal	SCAN
rs7556304	RP11-263K19.4	cis	Whole Blood	GTEx
rs7556304	GBA	cis	Esophagus Mucosa	GTEx
rs7556304	GBA	cis	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155134200-155145000	Weak transcription	Small Intestine	intestine
2	chr1:155138200-155139600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
3	chr1:155138200-155139600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr1:155138200-155140400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155138200-155140400	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:155138200-155140600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155138200-155140600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:155138200-155140600	Enhancers	HUVEC	blood vessel
9	chr1:155138400-155139600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:155138400-155139800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr1:155138400-155140000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155138400-155140000	Enhancers	Right Ventricle	heart
13	chr1:155138400-155140200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:155138400-155140400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:155138400-155140400	Enhancers	Left Ventricle	heart
16	chr1:155138400-155140600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:155138400-155140600	Enhancers	Placenta	Placenta
18	chr1:155138400-155140600	Enhancers	Spleen	Spleen
19	chr1:155138400-155140800	Enhancers	Colonic Mucosa	Colon
20	chr1:155138600-155139600	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:155138600-155139600	Weak transcription	Right Atrium	heart
22	chr1:155138600-155140000	Bivalent Enhancer	Fetal Intestine Small	intestine
23	chr1:155138600-155140400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:155138600-155140400	Enhancers	Fetal Lung	lung
25	chr1:155138600-155140400	Enhancers	Pancreas	Pancrea
26	chr1:155138600-155140600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:155138800-155139600	Enhancers	Primary B cells from cord blood	blood
28	chr1:155138800-155139600	Bivalent Enhancer	Adipose Nuclei	Adipose
29	chr1:155138800-155139600	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:155138800-155139600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:155138800-155139800	Bivalent Enhancer	Fetal Thymus	thymus
32	chr1:155138800-155140000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr1:155138800-155140000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr1:155138800-155140000	Weak transcription	Hela-S3	cervix
35	chr1:155138800-155140200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:155138800-155140200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
37	chr1:155138800-155140400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:155138800-155140600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:155138800-155140600	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:155138800-155140600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:155138800-155140600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:155138800-155140800	Enhancers	Fetal Intestine Large	intestine
43	chr1:155139000-155139600	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:155139000-155139600	Active TSS	HepG2	liver
45	chr1:155139000-155139800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr1:155139000-155140600	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr1:155139000-155140600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr1:155139000-155140600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:155139200-155139600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:155139200-155139600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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