Variant report

Variant	rs7944999
Chromosome Location	chr11:66687863-66687864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66687308..66690521-chr11:66692688..66697038,8	K562	blood:
2	chr11:66687308..66690460-chr11:66693802..66697038,4	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1077256	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10791894	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs10791896	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227624	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs11227625	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227630	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530891	0.80[CEU][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap]
rs1901376	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930394	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs6591226	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs67156018	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107498	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7110302	0.91[JPT][hapmap]
rs7119682	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs746018	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs746019	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7935749	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7936290	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7952017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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
4	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
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7944999	EHBP1L1	cis	cerebellum	SCAN
rs7944999	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs7944999	CDC42BPG	cis	cerebellum	SCAN
rs7944999	B3GNT1	cis	parietal	SCAN
rs7944999	FGF4	cis	parietal	SCAN
rs7944999	PC	cis	cerebellum	SCAN
rs7944999	NXF1	cis	parietal	SCAN
rs7944999	SLC25A45	cis	parietal	SCAN
rs7944999	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs7944999	RPS6KA4	cis	cerebellum	SCAN
rs7944999	ACTN3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66674400-66689600	Weak transcription	NHLF	lung
2	chr11:66674600-66696400	Weak transcription	NHEK	skin
3	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:66675600-66699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:66676200-66688600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:66676800-66696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:66677200-66692000	Weak transcription	Pancreas	Pancrea
8	chr11:66678000-66688600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:66680600-66689000	Weak transcription	Brain Germinal Matrix	brain
10	chr11:66683200-66688600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:66683200-66698200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:66683400-66688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:66683400-66688600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:66683600-66688400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:66683600-66688600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:66683800-66692400	Weak transcription	Fetal Intestine Small	intestine
17	chr11:66684000-66688600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:66684000-66688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:66684000-66688800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:66685400-66702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:66685800-66688400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:66686000-66689000	Enhancers	K562	blood
23	chr11:66686200-66688400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr11:66686400-66688000	Enhancers	GM12878-XiMat	blood
25	chr11:66686400-66688200	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:66686800-66689400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:66687000-66688400	Enhancers	Brain Substantia Nigra	brain
28	chr11:66687000-66688800	Enhancers	Brain Angular Gyrus	brain
29	chr11:66687000-66689000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr11:66687000-66689000	Genic enhancers	Hela-S3	cervix
31	chr11:66687000-66689400	Enhancers	Brain Anterior Caudate	brain
32	chr11:66687000-66689600	Enhancers	Brain Hippocampus Middle	brain
33	chr11:66687200-66688000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:66687200-66688200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:66687200-66689200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:66687400-66688200	Strong transcription	Liver	Liver
37	chr11:66687400-66689400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr11:66687400-66689600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:66687400-66689600	Enhancers	Adipose Nuclei	Adipose
40	chr11:66687400-66689800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr11:66687400-66689800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr11:66687400-66696400	Weak transcription	HSMMtube	muscle
43	chr11:66687600-66688200	Enhancers	A549	lung
44	chr11:66687600-66689000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:66687600-66689000	Enhancers	Psoas Muscle	Psoas
46	chr11:66687600-66690400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:66687800-66688800	Weak transcription	Osteobl	bone
48	chr11:66687800-66689000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:66687800-66696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:66687800-66701400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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