Variant report

Variant	rs2075569
Chromosome Location	chr1:155209360-155209361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155174858..155180302-chr1:155209102..155215747,8	MCF-7	breast:
2	chr1:155161998..155167332-chr1:155208163..155212538,6	K562	blood:
3	chr1:155207800..155212678-chr1:155214121..155217855,6	K562	blood:
4	chr1:155209079..155212795-chr1:155212935..155216540,4	MCF-7	breast:
5	chr1:155196978..155198560-chr1:155209319..155211586,2	K562	blood:

Variant related genes	Relation type
ENSG00000169231	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000173171	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1045253	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046188	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1052176	0.82[ASN][1000 genomes]
rs1052177	0.82[ASN][1000 genomes]
rs1076556	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1078699	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796940	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908459	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264337	0.86[YRI][hapmap]
rs11264338	0.86[YRI][hapmap]
rs11264339	0.86[YRI][hapmap]
rs11264343	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264345	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264346	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264348	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264349	0.83[ASN][1000 genomes]
rs11264352	0.85[ASN][1000 genomes]
rs11264353	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264359	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs1142287	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11577338	0.86[ASN][1000 genomes]
rs12026638	0.84[CHB][hapmap]
rs12034326	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042020	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12044063	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12049375	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12406363	0.84[ASN][1000 genomes]
rs12407919	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12411216	0.81[AFR][1000 genomes]
rs12563994	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12723761	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12724449	0.85[ASN][1000 genomes]
rs12748155	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12749306	0.85[ASN][1000 genomes]
rs1546818	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1800438	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800442	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807042	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2009578	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049805	0.90[AFR][1000 genomes]
rs2066981	0.95[LWK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2071053	0.82[ASN][1000 genomes]
rs2072647	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2075566	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2075570	0.87[AFR][1000 genomes]
rs2236863	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2236864	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2242576	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2242577	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2297480	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2361536	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2361543	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28373017	0.92[ASN][1000 genomes]
rs28445596	0.89[AFR][1000 genomes]
rs28595322	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2974929	0.88[AFR][1000 genomes]
rs2974930	0.89[AFR][1000 genomes]
rs2974931	0.88[AFR][1000 genomes]
rs2974935	0.87[AFR][1000 genomes]
rs2974937	0.85[AFR][1000 genomes]
rs2990220	0.86[AFR][1000 genomes]
rs2990245	0.88[AFR][1000 genomes]
rs370545	0.84[AFR][1000 genomes]
rs3754485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814318	0.80[ASN][1000 genomes]
rs3814319	0.82[ASN][1000 genomes]
rs4043	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072037	0.82[LWK][hapmap];0.90[YRI][hapmap]
rs4421576	0.86[YRI][hapmap]
rs4460629	0.82[YRI][hapmap]
rs4620533	0.82[ASN][1000 genomes]
rs4971079	0.83[YRI][hapmap]
rs4971085	0.86[YRI][hapmap]
rs4971088	0.86[YRI][hapmap]
rs497829	0.90[AFR][1000 genomes]
rs56310840	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59352002	0.84[AMR][1000 genomes]
rs734073	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs734074	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs741756	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7520184	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7543234	0.81[AMR][1000 genomes]
rs7549276	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7554780	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7556304	0.86[YRI][hapmap]
rs760077	0.81[AFR][1000 genomes]
rs762488	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8847	0.82[ASN][1000 genomes]
rs914615	0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs932972	0.82[ASN][1000 genomes]
rs9628662	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729564	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
4	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
5	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
6	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
7	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
8	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
9	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
10	nsv870053	chr1:155180349-155212316	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	esv13606	chr1:155180489-155221243	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv1008748	chr1:155189148-155230610	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
13	nsv1011773	chr1:155189148-155234821	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
14	esv1793876	chr1:155194112-155212255	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
15	nsv8480	chr1:155206335-155214536	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
16	nsv947198	chr1:155206997-155226440	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2075569	SPRR4	cis	parietal	SCAN
rs2075569	GBA	cis	Esophagus Mucosa	GTEx
rs2075569	LAMTOR2	cis	lymphoblastoid	seeQTL
rs2075569	THBS3	cis	Whole Blood	GTEx
rs2075569	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs2075569	GBAP1	cis	Artery Tibial	GTEx
rs2075569	CRNN	cis	cerebellum	SCAN
rs2075569	RP11-263K19.4	cis	Whole Blood	GTEx
rs2075569	GBAP1	cis	Thyroid	GTEx
rs2075569	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2075569	RPRD2	cis	cerebellum	SCAN
rs2075569	OAZ3	cis	parietal	SCAN
rs2075569	GBAP1	cis	cerebellum	SCAN
rs2075569	GBAP1	cis	Esophagus Mucosa	GTEx
rs2075569	GBAP1	cis	parietal	SCAN
rs2075569	SNORA42	cis	parietal	SCAN
rs2075569	GBA///GBAP	Cis_1M	lymphoblastoid	RTeQTL
rs2075569	GBA	cis	lymphoblastoid	seeQTL
rs2075569	PKLR	cis	cerebellum	SCAN
rs2075569	EFNA1	cis	cerebellum	SCAN
rs2075569	GBA	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155197200-155212800	Weak transcription	Small Intestine	intestine
2	chr1:155198000-155209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:155198000-155210400	Weak transcription	A549	lung
4	chr1:155198000-155210400	Weak transcription	HMEC	breast
5	chr1:155198000-155210400	Weak transcription	HSMM	muscle
6	chr1:155198000-155210600	Weak transcription	Psoas Muscle	Psoas
7	chr1:155198000-155210800	Weak transcription	Fetal Kidney	kidney
8	chr1:155198200-155209600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:155198200-155209600	Weak transcription	Fetal Brain Male	brain
10	chr1:155198200-155210400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:155198200-155210400	Weak transcription	Stomach Mucosa	stomach
12	chr1:155198200-155210400	Weak transcription	NHEK	skin
13	chr1:155198200-155210800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:155198200-155210800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:155201200-155210400	Weak transcription	HepG2	liver
16	chr1:155201400-155210400	Weak transcription	K562	blood
17	chr1:155201400-155210600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:155201800-155210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:155202200-155210400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:155202600-155210400	Weak transcription	Right Atrium	heart
21	chr1:155202800-155210200	Weak transcription	Fetal Lung	lung
22	chr1:155203800-155210400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:155204600-155209400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:155204600-155209400	Strong transcription	Spleen	Spleen
25	chr1:155204600-155209600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:155204600-155209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:155204600-155209800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:155204600-155210000	Strong transcription	Fetal Intestine Small	intestine
29	chr1:155204800-155209800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:155205000-155209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:155205000-155209600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:155205000-155209800	Strong transcription	Adipose Nuclei	Adipose
33	chr1:155205000-155209800	Strong transcription	Thymus	Thymus
34	chr1:155205200-155209400	Strong transcription	Fetal Thymus	thymus
35	chr1:155205400-155209600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:155205400-155209800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:155205400-155210000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:155205600-155209400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:155205600-155209600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:155205600-155209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:155205600-155209600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:155205600-155209600	Genic enhancers	Placenta	Placenta
43	chr1:155205600-155209800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:155205600-155209800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:155205600-155210000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:155205600-155210000	Strong transcription	Fetal Intestine Large	intestine
47	chr1:155205600-155210200	Strong transcription	Fetal Stomach	stomach
48	chr1:155205600-155210400	Weak transcription	Brain Angular Gyrus	brain
49	chr1:155205800-155209400	Strong transcription	Primary T cells from cord blood	blood
50	chr1:155205800-155209600	Strong transcription	Fetal Muscle Leg	muscle

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