Variant report

Variant	rs12501502
Chromosome Location	chr4:57279167-57279168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57277811..57280010-chr4:57300306..57302094,2	MCF-7	breast:
2	chr4:57252177..57255146-chr4:57278604..57280682,2	MCF-7	breast:
3	chr4:57278722..57280888-chr4:57296778..57299271,2	MCF-7	breast:
4	chr4:57273341..57278355-chr4:57278652..57283436,7	K562	blood:

Variant related genes	Relation type
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10434444	0.90[YRI][hapmap]
rs10434445	0.83[EUR][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11133443	0.80[TSI][hapmap]
rs12498340	0.81[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs12501334	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12510712	0.83[EUR][1000 genomes]
rs12511770	0.81[AMR][1000 genomes]
rs1401907	0.90[JPT][hapmap]
rs1474179	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17086696	0.83[TSI][hapmap];0.81[YRI][hapmap]
rs1967559	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1983378	0.90[YRI][hapmap]
rs2049087	0.91[MEX][hapmap]
rs2271923	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28866881	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3796541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796548	0.80[TSI][hapmap]
rs4346704	0.80[AMR][1000 genomes]
rs4493603	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864579	0.81[YRI][hapmap]
rs4864583	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5010012	0.91[CEU][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs56392224	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58151706	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66810706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6819534	0.91[MEX][hapmap]
rs6820314	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs6829250	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832797	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6834696	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6836118	0.80[TSI][hapmap]
rs6846895	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7671868	0.95[JPT][hapmap]
rs8340	0.81[LWK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs9996593	0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12501502	AASDH	cis	parietal	SCAN
rs12501502	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs12501502	SRP72	cis	cerebellum	SCAN
rs12501502	AASDH	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
4	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
12	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
15	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57274200-57296400	Weak transcription	Dnd41	blood
17	chr4:57276200-57280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:57276800-57284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57277000-57279400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:57277000-57280200	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:57277000-57280200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:57277000-57280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:57277000-57287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:57277000-57287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:57277000-57289800	Weak transcription	Fetal Stomach	stomach
27	chr4:57277000-57290000	Weak transcription	Aorta	Aorta
28	chr4:57277000-57290200	Weak transcription	Ovary	ovary
29	chr4:57277000-57290800	Weak transcription	Right Atrium	heart
30	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:57277000-57300000	Weak transcription	HSMM	muscle
33	chr4:57277200-57280200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:57277200-57280200	Weak transcription	HMEC	breast
35	chr4:57277200-57280400	Weak transcription	NH-A	brain
36	chr4:57277200-57283000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:57277600-57279200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:57277800-57280000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:57277800-57280000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:57277800-57280200	Weak transcription	NHLF	lung
41	chr4:57277800-57280400	Weak transcription	Fetal Lung	lung
42	chr4:57277800-57298000	Weak transcription	A549	lung
43	chr4:57278000-57280200	Weak transcription	Osteobl	bone
44	chr4:57278000-57286800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:57278000-57286800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:57278000-57290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:57278000-57291600	Weak transcription	Brain Anterior Caudate	brain
48	chr4:57278000-57291600	Weak transcription	HepG2	liver
49	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
50	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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