Variant report

Variant	rs2167457
Chromosome Location	chr11:66642396-66642397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66636341..66639567-chr11:66640880..66645266,6	K562	blood:
2	chr11:66637880..66639721-chr11:66640429..66643042,2	K562	blood:
3	chr11:66640579..66644175-chr11:66648917..66652443,5	MCF-7	breast:
4	chr11:66634682..66638253-chr11:66640416..66642598,5	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10750790	0.86[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10791889	0.86[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs10791892	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10896139	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11227610	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2077432	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2187041	0.86[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2380760	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741194	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741364	0.86[ASW][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]
rs4008953	0.91[EUR][1000 genomes]
rs4576826	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4930184	0.81[EUR][1000 genomes]
rs4930390	0.86[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs6591222	0.90[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7103627	0.90[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7119426	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7120256	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7122539	0.83[TSI][hapmap]
rs714766	0.84[EUR][1000 genomes]
rs7570	0.95[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes]
rs7930203	0.86[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7948839	0.95[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs9971487	0.95[AMR][1000 genomes];0.94[EUR][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	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2167457	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs2167457	EHBP1L1	cis	cerebellum	SCAN
rs2167457	RARRES3	cis	parietal	SCAN
rs2167457	B3GNT1	cis	parietal	SCAN
rs2167457	C11orf80	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66624200-66645000	Weak transcription	Fetal Kidney	kidney
2	chr11:66625000-66648800	Weak transcription	Right Atrium	heart
3	chr11:66625400-66645400	Weak transcription	Fetal Lung	lung
4	chr11:66625400-66645800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:66625400-66648000	Weak transcription	Left Ventricle	heart
6	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:66625800-66650800	Weak transcription	Osteobl	bone
8	chr11:66627000-66643000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:66627400-66642400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:66627800-66650000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:66629800-66645600	Weak transcription	Pancreas	Pancrea
12	chr11:66630200-66645600	Weak transcription	NHLF	lung
13	chr11:66633600-66648000	Weak transcription	Psoas Muscle	Psoas
14	chr11:66636600-66648000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:66636800-66642400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:66636800-66642400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:66636800-66644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:66636800-66645600	Weak transcription	Fetal Thymus	thymus
19	chr11:66636800-66646400	Weak transcription	Stomach Mucosa	stomach
20	chr11:66636800-66647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:66636800-66647800	Weak transcription	Thymus	Thymus
22	chr11:66636800-66648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:66636800-66650800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:66637000-66643600	Weak transcription	K562	blood
25	chr11:66637200-66642400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:66637200-66644000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:66638000-66650000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:66638600-66650200	Weak transcription	Fetal Intestine Large	intestine
29	chr11:66639000-66646600	Weak transcription	Brain Germinal Matrix	brain
30	chr11:66639000-66648000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:66639000-66657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:66639200-66645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:66639200-66646000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:66639200-66646200	Weak transcription	Brain Substantia Nigra	brain
35	chr11:66639200-66646400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:66639200-66646600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:66639200-66647800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:66639200-66649600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:66639200-66649800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:66639200-66657400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr11:66639400-66642400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:66639400-66642400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:66639400-66642800	Weak transcription	Brain Anterior Caudate	brain
44	chr11:66639400-66643000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:66639400-66643200	Weak transcription	Fetal Muscle Leg	muscle
46	chr11:66639400-66643400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr11:66639400-66644400	Weak transcription	Gastric	stomach
48	chr11:66639400-66645400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:66639400-66645400	Weak transcription	HMEC	breast
50	chr11:66639400-66645600	Weak transcription	Placenta	Placenta

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