Variant report

Variant	rs1025921
Chromosome Location	chr10:4713705-4713706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:4711824..4713897-chr10:4774936..4777024,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1E2-7	chr10:4713638-4713851	NONHSAT011111
2	lnc-AKR1E2-7	chr10:4713568-4713851	NONHSAT011110
3	lnc-AKR1E2-7	chr10:4713638-4713851	FPKM1_group_2824_transcript_1

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10444199	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10508286	0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs10795195	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10904310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10904311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10904312	0.86[ASN][1000 genomes]
rs10904313	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10904316	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11252641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11252642	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11252646	0.85[ASN][1000 genomes]
rs11252648	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11252653	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12780788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[ASN][1000 genomes]
rs12782668	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1498270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1838239	0.86[YRI][hapmap]
rs2083873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[ASN][1000 genomes]
rs2088500	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs2165953	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165955	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2173368	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs313428	0.82[CEU][hapmap];0.95[EUR][1000 genomes]
rs313433	0.93[EUR][1000 genomes]
rs313455	0.89[CEU][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs313493	0.95[EUR][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	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv1798456	chr10:4689138-4731081	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1817443	chr10:4689138-4731081	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1831014	chr10:4689138-4731081	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1838419	chr10:4689138-4731081	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1805926	chr10:4689842-4720626	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1809203	chr10:4689842-4720626	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1840346	chr10:4689842-4720626	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1842933	chr10:4689842-4720626	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1848476	chr10:4689842-4720626	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv549865	chr10:4704709-4715476	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv549870	chr10:4708627-4715476	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1025921	GATA3	cis	cerebellum	SCAN
rs1025921	TUBAL3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4712600-4714000	Enhancers	NHDF-Ad	bronchial
2	chr10:4712600-4716200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr10:4712800-4714800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:4713000-4713800	Flanking Active TSS	A549	lung
5	chr10:4713000-4714000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:4713000-4714200	Strong transcription	HUVEC	blood vessel
7	chr10:4713000-4714400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:4713000-4714600	Enhancers	HSMM	muscle
9	chr10:4713000-4715000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:4713000-4715400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr10:4713000-4715400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr10:4713000-4715600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:4713200-4713800	Weak transcription	NHLF	lung
14	chr10:4713200-4714000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:4713200-4714000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr10:4713200-4714400	Flanking Active TSS	HMEC	breast
17	chr10:4713200-4714600	Enhancers	HSMMtube	muscle
18	chr10:4713200-4714800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:4713200-4714800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:4713200-4715600	Flanking Active TSS	NHEK	skin
21	chr10:4713400-4713800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:4713400-4713800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:4713600-4713800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr10:4713600-4714000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr10:4713600-4714200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:4713600-4714200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:4713600-4714200	Active TSS	Left Ventricle	heart
28	chr10:4713600-4714200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr10:4713600-4714200	Flanking Active TSS	NH-A	brain
30	chr10:4713600-4714600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:4713600-4714600	Flanking Active TSS	Osteobl	bone
32	chr10:4713600-4714800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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