Variant report

Variant	rs7540181
Chromosome Location	chr1:225719371-225719372
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225717290..225720018-chr1:225721925..225724393,2	K562	blood:
2	chr1:225718758..225721706-chr1:225723433..225725364,3	K562	blood:
3	chr1:225712577..225715165-chr1:225716923..225719442,2	MCF-7	breast:
4	chr1:225716258..225718106-chr1:225719282..225721032,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10753406	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10799311	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10799314	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799316	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs10799317	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799318	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10915830	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915833	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915834	0.93[EUR][1000 genomes]
rs10915837	0.81[ASN][1000 genomes]
rs10915839	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915847	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584675	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12028305	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12729655	0.81[ASN][1000 genomes]
rs2639703	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2639716	0.83[EUR][1000 genomes]
rs2657564	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2657569	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2840958	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2840967	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2840968	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs3820226	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856156	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653643	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476540	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs487591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs498350	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510293	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511649	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516249	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551996	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554992	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561656	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576861	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426076	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6668770	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676201	0.81[ASN][1000 genomes]
rs6678806	0.81[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6751	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712062	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515907	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515963	0.81[ASN][1000 genomes]
rs7524766	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541598	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555139	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs812523	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs947034	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9804142	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7540181	RP11-496N12.9	cis	Thyroid	GTEx
rs7540181	LBR	cis	Artery Tibial	GTEx
rs7540181	ENAH	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
3	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
5	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:225700000-225726400	Weak transcription	HMEC	breast
7	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
9	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
10	chr1:225704200-225721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:225705800-225726600	Weak transcription	NHEK	skin
13	chr1:225707200-225726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:225707200-225755000	Weak transcription	Gastric	stomach
15	chr1:225707400-225726600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:225709000-225721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:225709200-225720000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:225711400-225726600	Weak transcription	Fetal Brain Female	brain
19	chr1:225711600-225720600	Weak transcription	Fetal Intestine Small	intestine
20	chr1:225711600-225720600	Weak transcription	HSMMtube	muscle
21	chr1:225711600-225721200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:225712400-225729600	Weak transcription	Right Ventricle	heart
23	chr1:225713600-225719400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr1:225713800-225721000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:225714800-225729600	Weak transcription	Ovary	ovary
26	chr1:225715000-225721000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:225715200-225719400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:225715600-225720600	Weak transcription	Fetal Heart	heart
29	chr1:225715600-225720800	Weak transcription	Fetal Brain Male	brain
30	chr1:225715600-225721000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:225716000-225720000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:225716200-225720000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:225716200-225720600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:225716200-225720600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:225716200-225720800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:225716200-225720800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:225716600-225721000	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:225716800-225726400	Weak transcription	Left Ventricle	heart
39	chr1:225716800-225726400	Weak transcription	Psoas Muscle	Psoas
40	chr1:225717600-225726600	Weak transcription	NHDF-Ad	bronchial
41	chr1:225717600-225732000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:225717800-225720600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:225717800-225720600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:225717800-225720800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:225717800-225720800	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:225717800-225722400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:225717800-225722800	Weak transcription	NH-A	brain
49	chr1:225717800-225725800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:225717800-225729600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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