Variant report

Variant	rs1421750
Chromosome Location	chr5:127212228-127212229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:127211793..127217903-chr5:127417278..127420388,8	MCF-7	breast:
2	chr5:127208944..127216752-chr5:127415805..127421659,21	MCF-7	breast:
3	chr5:127211016..127213453-chr5:127292897..127295874,2	MCF-7	breast:
4	chr5:127210281..127212908-chr5:127422377..127423931,2	MCF-7	breast:
5	chr5:127209915..127212381-chr5:127451005..127452800,2	MCF-7	breast:
6	chr5:127210963..127213061-chr5:127280494..127282424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10042555	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058856	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs111941	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs111942	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs122730	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs122731	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs122734	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12332194	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332385	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332386	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332552	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421748	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421749	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421751	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151853	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151856	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151858	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151859	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151882	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs1520247	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173444	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187381	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193495	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2006195	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108653	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409033	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245156	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs245160	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245172	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245173	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245174	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245175	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245181	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs245186	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs245192	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs245195	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs245221	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs245237	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2544779	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2544780	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681512	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2764766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1421750	SLC12A2	cis	cerebellum	SCAN
rs1421750	SLC27A6	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127194200-127213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:127207000-127213600	Weak transcription	Gastric	stomach
3	chr5:127207000-127213800	Weak transcription	Left Ventricle	heart
4	chr5:127207800-127220800	Weak transcription	Brain Angular Gyrus	brain
5	chr5:127208000-127212800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:127208400-127212400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:127208400-127212400	Weak transcription	Right Atrium	heart
8	chr5:127209600-127213600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:127211000-127212400	Enhancers	Brain Hippocampus Middle	brain
10	chr5:127211000-127212400	Enhancers	Brain Substantia Nigra	brain
11	chr5:127211000-127212400	Enhancers	Fetal Lung	lung
12	chr5:127211000-127212400	Enhancers	HSMMtube	muscle
13	chr5:127211000-127212600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr5:127211000-127212600	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:127211000-127212600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr5:127211000-127212800	Enhancers	Fetal Heart	heart
17	chr5:127211200-127212400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:127211200-127212400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:127211200-127212400	Enhancers	Colon Smooth Muscle	Colon
20	chr5:127211200-127212400	Enhancers	HSMM	muscle
21	chr5:127211200-127212400	Enhancers	Osteobl	bone
22	chr5:127211200-127212600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:127211200-127212600	Enhancers	Fetal Intestine Small	intestine
24	chr5:127211200-127212600	Enhancers	NHLF	lung
25	chr5:127211400-127212400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:127211400-127212400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:127211400-127212400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:127211400-127212400	Enhancers	Fetal Muscle Leg	muscle
29	chr5:127211400-127212400	Enhancers	Psoas Muscle	Psoas
30	chr5:127211400-127212400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr5:127211400-127212600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:127211400-127212600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:127211400-127212600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:127211400-127212600	Enhancers	Fetal Intestine Large	intestine
35	chr5:127211400-127212600	Enhancers	Fetal Kidney	kidney
36	chr5:127211400-127212600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr5:127211400-127214000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:127211600-127212600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:127211600-127212600	Enhancers	HMEC	breast
40	chr5:127211600-127216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:127211600-127220600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:127211800-127212400	Enhancers	GM12878-XiMat	blood
43	chr5:127211800-127212400	Enhancers	Hela-S3	cervix
44	chr5:127211800-127212600	Enhancers	Stomach Smooth Muscle	stomach
45	chr5:127211800-127213000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr5:127211800-127213200	Weak transcription	HepG2	liver
47	chr5:127211800-127213600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:127211800-127213600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:127211800-127213600	Weak transcription	Fetal Stomach	stomach
50	chr5:127211800-127213800	Weak transcription	Brain Inferior Temporal Lobe	brain

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