Variant report

Variant	rs1925033
Chromosome Location	chr1:158015996-158015997
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158014548..158016120-chr1:158017209..158018949,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10796989	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10796990	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10796991	0.89[CEU][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10796992	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10796993	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10796994	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10908613	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10908614	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264879	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap]
rs11580742	1.00[CHD][hapmap]
rs11585913	1.00[CHD][hapmap]
rs12047033	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17419936	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs17419999	0.89[CEU][hapmap]
rs17453741	0.89[CEU][hapmap]
rs4246542	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971122	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427417	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs6686246	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7549283	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1005196	chr1:158015996-158065522	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1925033	KIRREL	cis	cerebellum	SCAN
rs1925033	GATAD2B	cis	cerebellum	SCAN
rs1925033	ASH1L	cis	cerebellum	SCAN
rs1925033	SPRR3	cis	cerebellum	SCAN
rs1925033	DCST1	cis	cerebellum	SCAN
rs1925033	VPS39	trans	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
3	chr1:158002400-158025400	Weak transcription	Fetal Brain Female	brain
4	chr1:158008000-158019600	Weak transcription	Colonic Mucosa	Colon
5	chr1:158008200-158018400	Weak transcription	Spleen	Spleen
6	chr1:158008200-158023000	Weak transcription	A549	lung
7	chr1:158008200-158024600	Weak transcription	Placenta	Placenta
8	chr1:158009400-158024400	Weak transcription	Hela-S3	cervix
9	chr1:158009600-158022600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:158010000-158023000	Weak transcription	HSMM	muscle
11	chr1:158010200-158020600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:158011000-158017200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:158012200-158019800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:158012400-158017200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:158012800-158016800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:158012800-158017000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:158012800-158017200	Enhancers	Lung	lung
18	chr1:158013000-158016200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:158013000-158016400	Enhancers	Fetal Muscle Leg	muscle
20	chr1:158013000-158016600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:158013000-158016600	Enhancers	Right Atrium	heart
22	chr1:158013000-158017200	Enhancers	Ovary	ovary
23	chr1:158013000-158020600	Enhancers	Fetal Lung	lung
24	chr1:158013200-158017400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:158013400-158017800	Enhancers	Adipose Nuclei	Adipose
26	chr1:158013400-158020600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:158013600-158020600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:158013600-158025600	Weak transcription	Brain Germinal Matrix	brain
29	chr1:158013800-158017000	Strong transcription	NHEK	skin
30	chr1:158013800-158027000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:158014000-158016800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:158014200-158018200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:158014200-158018800	Enhancers	Fetal Kidney	kidney
34	chr1:158014600-158016000	Enhancers	Osteobl	bone
35	chr1:158014600-158016200	Enhancers	Colon Smooth Muscle	Colon
36	chr1:158014600-158016200	Enhancers	NH-A	brain
37	chr1:158014600-158016600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:158014600-158016600	Enhancers	NHDF-Ad	bronchial
39	chr1:158014600-158016800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:158014600-158017600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:158014800-158016000	Enhancers	Pancreas	Pancrea
42	chr1:158014800-158016000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
43	chr1:158014800-158016000	Enhancers	HMEC	breast
44	chr1:158014800-158016200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:158014800-158016200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:158014800-158016200	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:158014800-158016200	Enhancers	NHLF	lung
48	chr1:158014800-158016400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:158014800-158016600	Enhancers	H9 Cell Line	embryonic stem cell
50	chr1:158014800-158016600	Enhancers	HUES48 Cell Line	embryonic stem cell

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