Variant report

Variant	rs2764766
Chromosome Location	chr5:127213625-127213626
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127213582..127214540-chr5:127536708..127537793,3	K562	blood:
2	chr5:127211793..127217903-chr5:127417278..127420388,8	MCF-7	breast:
3	chr5:127154107..127155724-chr5:127212443..127214983,2	MCF-7	breast:
4	chr5:127212385..127215145-chr5:127219355..127222619,3	MCF-7	breast:
5	chr5:127208944..127216752-chr5:127415805..127421659,21	MCF-7	breast:
6	chr5:127213531..127214118-chr5:127244516..127245280,2	MCF-7	breast:
7	chr5:127213246..127215521-chr5:127308209..127310216,2	MCF-7	breast:
8	chr5:127212523..127214164-chr5:127301948..127304809,2	MCF-7	breast:

No data

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	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058856	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs111941	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs111942	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs122730	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs122731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs122734	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332194	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332386	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332552	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421748	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421749	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421750	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]
rs1421751	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151853	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151858	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151859	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151882	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs1520247	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173444	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187381	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193495	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2006195	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108653	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409033	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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];0.91[ASN][1000 genomes]
rs245160	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs245167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245172	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245174	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245175	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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];0.94[ASN][1000 genomes]
rs245237	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2544779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544780	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs2764766	SLC12A2	cis	cerebellum	SCAN
rs2764766	SLC27A6	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127194200-127213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:127207000-127213800	Weak transcription	Left Ventricle	heart
3	chr5:127207800-127220800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:127211400-127214000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:127211600-127216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:127211600-127220600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:127211800-127213800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:127211800-127213800	Weak transcription	HUVEC	blood vessel
9	chr5:127211800-127214000	Enhancers	Duodenum Mucosa	Duodenum
10	chr5:127211800-127214400	Enhancers	A549	lung
11	chr5:127212000-127214400	Enhancers	Stomach Mucosa	stomach
12	chr5:127212200-127219600	Weak transcription	Small Intestine	intestine
13	chr5:127212400-127217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:127212400-127217200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:127212400-127220200	Weak transcription	Psoas Muscle	Psoas
16	chr5:127212400-127220800	Weak transcription	Fetal Lung	lung
17	chr5:127212600-127213800	Weak transcription	NHLF	lung
18	chr5:127212600-127214000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:127212600-127218400	Weak transcription	Fetal Kidney	kidney
20	chr5:127213000-127213800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:127213000-127214000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr5:127213000-127214400	Enhancers	Fetal Intestine Large	intestine
23	chr5:127213000-127214400	Enhancers	Fetal Intestine Small	intestine
24	chr5:127213000-127214400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr5:127213200-127213800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:127213200-127213800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:127213200-127214000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:127213200-127214000	Enhancers	HepG2	liver
29	chr5:127213200-127214200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:127213200-127214200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:127213400-127214200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:127213600-127213800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr5:127213600-127213800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:127213600-127213800	Enhancers	Gastric	stomach
35	chr5:127213600-127213800	Enhancers	GM12878-XiMat	blood
36	chr5:127213600-127213800	Enhancers	HMEC	breast
37	chr5:127213600-127214000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:127213600-127214000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr5:127213600-127214000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:127213600-127214000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr5:127213600-127214000	Enhancers	Brain Anterior Caudate	brain
42	chr5:127213600-127214000	Enhancers	Brain Hippocampus Middle	brain
43	chr5:127213600-127214400	Enhancers	Brain Substantia Nigra	brain

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