Variant report

Variant	rs12135266
Chromosome Location	chr1:93932949-93932950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1055654	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10874786	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10874790	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164924	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11164936	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164938	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164943	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042552	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12044883	0.83[JPT][hapmap]
rs12123339	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12133576	0.90[JPT][hapmap]
rs12138486	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs12406245	0.90[JPT][hapmap]
rs12742850	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1426318	0.90[JPT][hapmap]
rs1559828	0.90[JPT][hapmap]
rs1812668	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs237438	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs237439	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2391271	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2624436	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624439	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35102250	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3767964	0.90[JPT][hapmap]
rs3767967	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4847240	0.90[JPT][hapmap]
rs4847245	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847428	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847429	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847431	0.89[CEU][hapmap];0.83[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7525248	0.90[JPT][hapmap]
rs7546702	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7551016	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs771481	0.82[CEU][hapmap]
rs8179368	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12135266	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12135266	TMED5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93915200-93935800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93915200-93937000	Weak transcription	Esophagus	oesophagus
3	chr1:93915200-93937000	Weak transcription	Lung	lung
4	chr1:93916400-93934800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:93917600-93937200	Weak transcription	Fetal Brain Male	brain
6	chr1:93919800-93937000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:93920000-93936800	Weak transcription	NH-A	brain
8	chr1:93920000-93943800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:93920400-93936600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:93921200-93936000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:93921200-93936600	Weak transcription	HUVEC	blood vessel
12	chr1:93921200-93937000	Weak transcription	Left Ventricle	heart
13	chr1:93921200-93939800	Weak transcription	Right Ventricle	heart
14	chr1:93922600-93944000	Weak transcription	Gastric	stomach
15	chr1:93924000-93933200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:93924400-93937000	Weak transcription	Fetal Lung	lung
17	chr1:93925800-93937000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:93926000-93937200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:93926800-93936000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:93927200-93936400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:93927600-93935600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:93927600-93943800	Weak transcription	Pancreas	Pancrea
23	chr1:93928400-93936600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:93929000-93946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:93929400-93936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:93930000-93937200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:93930200-93933600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:93930600-93943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:93930800-93933200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:93932400-93933400	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr1:93932800-93933200	ZNF genes & repeats	Fetal Kidney	kidney
32	chr1:93932800-93933400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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