Variant report

Variant	rs2670462
Chromosome Location	chr1:227432923-227432924
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10495253	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799381	0.80[AMR][1000 genomes]
rs10916104	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12039370	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12139758	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs1320494	0.80[AMR][1000 genomes]
rs1483	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2102634	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2482454	0.83[AMR][1000 genomes]
rs2492630	0.80[AMR][1000 genomes]
rs2670471	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2718193	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2813947	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813948	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813950	0.89[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813965	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813967	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813969	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813970	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754418	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4351610	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4500279	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653479	0.80[AMR][1000 genomes]
rs4653813	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs485234	0.81[AMR][1000 genomes]
rs488104	0.83[AMR][1000 genomes]
rs498020	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs56219094	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834571	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648877	0.80[AMR][1000 genomes]
rs6662583	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6682472	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6682642	0.80[AMR][1000 genomes]
rs6685823	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs6692080	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697665	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6699828	0.80[AMR][1000 genomes]
rs689094	0.83[AMR][1000 genomes]
rs694740	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs7412928	0.82[EUR][1000 genomes]
rs7512409	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521110	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543579	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7549520	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2670462	MIXL1	cis	parietal	SCAN
rs2670462	ITPKB	cis	lymphoblastoid	seeQTL
rs2670462	C1orf65	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:227414200-227453800	Weak transcription	HSMM	muscle
6	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
8	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:227425400-227445200	Weak transcription	Osteobl	bone
10	chr1:227427200-227433200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:227430600-227433000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:227430600-227433400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:227430600-227434000	Enhancers	Brain Anterior Caudate	brain
14	chr1:227430600-227434000	Enhancers	Pancreas	Pancrea
15	chr1:227430600-227434600	Enhancers	Fetal Heart	heart
16	chr1:227430800-227433000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:227430800-227433000	Enhancers	HUVEC	blood vessel
18	chr1:227430800-227433200	Enhancers	Ovary	ovary
19	chr1:227430800-227434200	Enhancers	Gastric	stomach
20	chr1:227431000-227433600	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:227431400-227433000	Enhancers	Psoas Muscle	Psoas
22	chr1:227431400-227434000	Enhancers	Brain Hippocampus Middle	brain
23	chr1:227431400-227434200	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:227431600-227435400	Weak transcription	NHLF	lung
25	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
26	chr1:227431800-227433000	Enhancers	Fetal Intestine Small	intestine
27	chr1:227431800-227439200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:227431800-227443000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:227432000-227433000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:227432000-227433600	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:227432000-227434400	Enhancers	Brain Substantia Nigra	brain
32	chr1:227432000-227434800	Enhancers	HepG2	liver
33	chr1:227432000-227435200	Weak transcription	Fetal Brain Female	brain
34	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
35	chr1:227432200-227433000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:227432200-227433200	Enhancers	Stomach Mucosa	stomach
37	chr1:227432200-227434200	Enhancers	Right Atrium	heart
38	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:227432400-227433000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr1:227432400-227433000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:227432400-227433400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:227432400-227433600	Enhancers	Small Intestine	intestine
43	chr1:227432400-227434000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:227432400-227434000	Weak transcription	Placenta	Placenta
45	chr1:227432400-227434200	Enhancers	Adipose Nuclei	Adipose
46	chr1:227432400-227434200	Enhancers	Left Ventricle	heart
47	chr1:227432400-227434200	Enhancers	Right Ventricle	heart
48	chr1:227432400-227434800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:227432400-227434800	Enhancers	HMEC	breast
50	chr1:227432400-227435000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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