Variant report

Variant	rs12035524
Chromosome Location	chr1:155667102-155667103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155098358..155100782-chr1:155664787..155667283,2	K562	blood:
2	chr1:155656565..155660782-chr1:155662182..155667108,10	MCF-7	breast:
3	chr1:155656893..155661917-chr1:155662515..155668604,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163374	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000132676	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10752611	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs10908469	0.91[JPT][hapmap]
rs10908470	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs10908471	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs10908472	0.82[AMR][1000 genomes]
rs10908479	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908481	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.80[ASN][1000 genomes]
rs10908482	0.80[ASN][1000 genomes]
rs11264380	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs11264381	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs11264383	0.82[AMR][1000 genomes]
rs11264387	0.80[CEU][hapmap];0.88[GIH][hapmap];0.83[MKK][hapmap]
rs11264397	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264398	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11264409	0.80[ASN][1000 genomes]
rs12022088	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12039893	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12040100	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12047626	0.84[AMR][1000 genomes]
rs12047756	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12091730	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12143948	0.91[JPT][hapmap]
rs12740629	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12744132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746592	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs12758945	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360554	0.91[JPT][hapmap]
rs1556488	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs2048431	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175391	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28662267	0.83[ASN][1000 genomes]
rs34124416	0.81[EUR][1000 genomes]
rs34620961	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348186	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348192	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs348196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35615695	0.91[JPT][hapmap]
rs3738590	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820594	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs3851912	0.81[EUR][1000 genomes]
rs3892792	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs4278368	0.81[ASN][1000 genomes]
rs475550	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490608	0.85[ASN][1000 genomes]
rs4971095	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427286	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.91[JPT][hapmap]
rs6665227	0.80[ASN][1000 genomes]
rs6672128	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688636	0.91[JPT][hapmap]
rs6696888	0.91[JPT][hapmap]
rs670876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs678157	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs708611	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs7521594	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541060	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.91[JPT][hapmap]
rs822490	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs860295	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs9426933	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	41 gene(s)	inside rSNPs	diseases
8	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	nsv3054	chr1:155653835-155673509	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
12	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12035524	LCE1C	cis	parietal	SCAN
rs12035524	YY1AP1	cis	cerebellum	SCAN
rs12035524	LCE1F	cis	cerebellum	SCAN
rs12035524	FDPS	cis	parietal	SCAN
rs12035524	GBAP1	cis	cerebellum	SCAN
rs12035524	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12035524	ADAM15	cis	multi-tissue	Pritchard
rs12035524	SPRR2D	cis	parietal	SCAN
rs12035524	YY1AP1	cis	parietal	SCAN
rs12035524	GBAP1	cis	parietal	SCAN
rs12035524	GPATCH4	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155659400-155668200	Weak transcription	Aorta	Aorta
2	chr1:155660000-155667600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:155660200-155668000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:155660200-155698800	Weak transcription	NHLF	lung
5	chr1:155660400-155668400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:155660400-155671000	Weak transcription	Esophagus	oesophagus
7	chr1:155660400-155675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:155660400-155682800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:155660400-155688800	Weak transcription	Lung	lung
10	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
11	chr1:155660600-155668000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:155660600-155679000	Weak transcription	Fetal Brain Female	brain
13	chr1:155660600-155680200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:155660800-155682600	Weak transcription	Spleen	Spleen
15	chr1:155661600-155688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
17	chr1:155661800-155668400	Weak transcription	NH-A	brain
18	chr1:155662200-155669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:155662200-155682000	Weak transcription	HSMMtube	muscle
20	chr1:155662400-155668400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:155662400-155682800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:155662400-155685600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:155662600-155669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:155662600-155673800	Weak transcription	HMEC	breast
25	chr1:155662800-155668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:155663000-155679400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:155663000-155681200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:155663200-155667200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:155663200-155668200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:155663200-155668200	Weak transcription	Osteobl	bone
31	chr1:155663200-155668600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:155663200-155675800	Weak transcription	HSMM	muscle
33	chr1:155663200-155679200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:155663400-155682600	Weak transcription	Primary B cells from cord blood	blood
36	chr1:155664400-155674600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:155664400-155678800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:155664400-155679000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:155664600-155667200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:155664800-155667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:155665000-155673600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:155665000-155678600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:155665200-155667200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:155665200-155667200	Enhancers	Brain Germinal Matrix	brain
45	chr1:155665200-155668000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:155665200-155668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:155665200-155668600	Weak transcription	Fetal Heart	heart
48	chr1:155665200-155673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:155665200-155676000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:155665200-155685800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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