Variant report

Variant	rs1230154
Chromosome Location	chr4:99988659-99988660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99849268..99851991-chr4:99985769..99989204,3	K562	blood:
2	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
3	chr4:99849436..99851753-chr4:99986729..99991688,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADH5-1	chr4:99988407-99989276	ENSG00000272777.1

Variant related genes	Relation type
ENSG00000263923	Chromatin interaction
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000151247	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10017466	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs1042364	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs1042365	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs1126670	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs1126671	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs1126672	0.83[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs1126673	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs1139490	0.82[AMR][1000 genomes]
rs1154401	0.86[AMR][1000 genomes]
rs1154405	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs1154410	0.83[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs1154412	0.93[GIH][hapmap]
rs11547772	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1230155	0.81[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230157	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs1230158	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230164	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230165	0.86[GIH][hapmap];1.00[ASN][1000 genomes]
rs13110176	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13110764	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13112176	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs1311615	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs1311616	0.83[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1311617	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs13129488	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13133647	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13138294	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13143133	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs1377689	0.87[CEU][hapmap]
rs13832	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1453874	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs17217949	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218003	0.83[CEU][hapmap]
rs17218073	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218108	0.83[CEU][hapmap]
rs17218141	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218162	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218239	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218288	0.83[CEU][hapmap]
rs17218560	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17218602	0.82[CEU][hapmap]
rs17817359	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17817868	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17817958	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2602895	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2602896	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2851246	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2851247	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2851248	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs2851270	0.81[AMR][1000 genomes]
rs2851274	0.84[AMR][1000 genomes]
rs2851277	0.86[CEU][hapmap]
rs2851278	0.87[CEU][hapmap]
rs29001203	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs3018047	0.87[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs3018048	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs34936974	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs4699710	0.86[AMR][1000 genomes]
rs4699712	0.83[CEU][hapmap]
rs4699713	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs4699714	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs4699716	0.82[TSI][hapmap]
rs4699717	0.86[GIH][hapmap]
rs6532795	0.84[AMR][1000 genomes]
rs6532796	0.83[AMR][1000 genomes]
rs6532798	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs6822348	0.84[AMR][1000 genomes]
rs6831257	0.83[AMR][1000 genomes]
rs6831352	0.86[AMR][1000 genomes]
rs6837685	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs6848050	0.86[AMR][1000 genomes]
rs7658118	0.89[AFR][1000 genomes]
rs7658279	0.89[AFR][1000 genomes]
rs7669636	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs7670060	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs7670241	0.83[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs7694646	0.82[CEU][hapmap]
rs896992	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1230154	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:99971000-99988800	Weak transcription	Fetal Brain Male	brain
5	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
6	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
7	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:99976000-99989800	Weak transcription	Fetal Brain Female	brain
9	chr4:99976400-99992800	Weak transcription	Aorta	Aorta
10	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:99977400-99991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:99977400-99992800	Weak transcription	Brain Substantia Nigra	brain
13	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
14	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
15	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
18	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:99979800-99992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:99980000-99992600	Weak transcription	Colonic Mucosa	Colon
23	chr4:99980000-99993000	Weak transcription	Ovary	ovary
24	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
25	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:99980200-99993000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:99980400-99991400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:99981000-99992400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:99981200-99992400	Weak transcription	Brain Germinal Matrix	brain
30	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:99982000-99990000	Weak transcription	Placenta	Placenta
32	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
34	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:99982600-99991600	Weak transcription	NHLF	lung
36	chr4:99982600-99992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:99982600-99992400	Weak transcription	NHEK	skin
38	chr4:99982600-99992600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:99982800-99989800	Weak transcription	Fetal Stomach	stomach
41	chr4:99982800-99993000	Weak transcription	Left Ventricle	heart
42	chr4:99982800-99996000	Weak transcription	Gastric	stomach
43	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
44	chr4:99983000-99991600	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
46	chr4:99983200-99992400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:99983200-99992800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:99983400-99989200	Weak transcription	Fetal Muscle Trunk	muscle

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