Variant report

Variant	rs1220389
Chromosome Location	chr1:9979185-9979186
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	chr1:9971162..9973726-chr1:9979028..9981341,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10779734	0.81[ASN][1000 genomes]
rs11121512	0.82[ASN][1000 genomes]
rs11828	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140009	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140015	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140058	0.86[ASN][1000 genomes]
rs1220397	0.85[ASN][1000 genomes]
rs1220399	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1220400	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1220402	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1220420	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1220421	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1220424	0.86[ASN][1000 genomes]
rs1234694	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1628143	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1660733	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2890358	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2919694	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3003378	0.83[ASN][1000 genomes]
rs3013783	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3013784	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34851031	0.83[ASN][1000 genomes]
rs6541073	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6661806	0.86[ASN][1000 genomes]
rs6663108	0.81[ASN][1000 genomes]
rs6664631	0.84[ASN][1000 genomes]
rs7517360	0.86[ASN][1000 genomes]
rs7517812	0.83[ASN][1000 genomes]
rs7539191	0.80[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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	35 gene(s)	inside rSNPs	diseases
5	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1220389	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971200-9981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:9971400-9982600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:9971400-9987400	Weak transcription	Fetal Stomach	stomach
4	chr1:9971400-9993600	Weak transcription	Aorta	Aorta
5	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
6	chr1:9971600-9980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:9971600-9988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:9971600-9991200	Weak transcription	NHEK	skin
9	chr1:9971800-9985600	Weak transcription	Primary T cells from cord blood	blood
10	chr1:9971800-9986600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:9971800-9987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:9971800-9987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:9971800-9989000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:9971800-9991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:9972600-9982400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:9972600-9988000	Weak transcription	Lung	lung
17	chr1:9972600-9988600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
19	chr1:9972800-9989600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:9973000-9988400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:9975000-9982200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
23	chr1:9977000-9982200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:9977000-9991800	Weak transcription	Brain Germinal Matrix	brain
25	chr1:9977200-9982000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:9977200-9982200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:9977400-9980800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:9977400-9982200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:9978200-9990200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:9978600-9984800	Weak transcription	HepG2	liver

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