Variant report

Variant	rs1230155
Chromosome Location	chr4:99989259-99989260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
2	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
ENSG00000238449	Chromatin interaction
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000263923	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10017466	0.80[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap]
rs1126670	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs1126671	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs1126673	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs1154400	0.84[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap]
rs1154401	0.96[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1154403	0.86[AMR][1000 genomes]
rs1154412	0.81[GIH][hapmap]
rs12106	0.92[AFR][1000 genomes]
rs1230154	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	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230157	0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs1230158	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230164	0.87[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1230165	1.00[ASN][1000 genomes]
rs1230167	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12697	0.84[ASW][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1311620	0.88[CEU][hapmap];0.91[YRI][hapmap]
rs13832	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1540053	0.81[GIH][hapmap]
rs2602856	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2851270	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851274	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851277	0.82[CEU][hapmap]
rs28730602	0.87[AFR][1000 genomes]
rs28730632	0.88[AFR][1000 genomes]
rs4699700	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6532796	0.81[AMR][1000 genomes]
rs6532798	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs6831257	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6837685	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs7669660	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7683704	0.93[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7684735	0.94[AFR][1000 genomes]
rs896992	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1230155	ADH5	cis	cerebellum	SCAN
rs1230155	ADH5	cis	Whole Blood	GTEx
rs1230155	METAP1	cis	cerebellum	SCAN

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	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
6	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:99976000-99989800	Weak transcription	Fetal Brain Female	brain
8	chr4:99976400-99992800	Weak transcription	Aorta	Aorta
9	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:99977400-99991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:99977400-99992800	Weak transcription	Brain Substantia Nigra	brain
12	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
13	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
17	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:99979800-99992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:99980000-99992600	Weak transcription	Colonic Mucosa	Colon
22	chr4:99980000-99993000	Weak transcription	Ovary	ovary
23	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
24	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:99980200-99993000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:99980400-99991400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:99981000-99992400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:99981200-99992400	Weak transcription	Brain Germinal Matrix	brain
29	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:99982000-99990000	Weak transcription	Placenta	Placenta
31	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
33	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:99982600-99991600	Weak transcription	NHLF	lung
35	chr4:99982600-99992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:99982600-99992400	Weak transcription	NHEK	skin
37	chr4:99982600-99992600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:99982800-99989800	Weak transcription	Fetal Stomach	stomach
40	chr4:99982800-99993000	Weak transcription	Left Ventricle	heart
41	chr4:99982800-99996000	Weak transcription	Gastric	stomach
42	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
43	chr4:99983000-99991600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
45	chr4:99983200-99992400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:99983200-99992800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:99983400-99990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:99983400-99991000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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