Variant report

Variant	rs2923944
Chromosome Location	chr11:3971079-3971080
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	chr11:3966514..3968687-chr11:3969725..3973118,3	K562	blood:
2	chr11:3952774..3955430-chr11:3970846..3973149,2	K562	blood:

Variant related genes	Relation type
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10742189	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10742223	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10767706	0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10767807	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10835301	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11030224	0.89[CEU][hapmap]
rs11030264	0.96[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11030394	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030536	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11030842	0.81[GIH][hapmap];0.93[TSI][hapmap]
rs11030907	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs11604649	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12419208	0.91[AFR][1000 genomes]
rs12803023	0.86[ASW][hapmap]
rs1372804	0.86[GIH][hapmap];0.93[TSI][hapmap]
rs1372805	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17193797	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980412	0.83[MKK][hapmap]
rs2304891	0.93[ASW][hapmap];1.00[LWK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs2735691	0.83[MKK][hapmap]
rs2920139	0.91[AFR][1000 genomes]
rs2920144	0.93[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2923945	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2923948	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2923953	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2923956	0.93[ASW][hapmap];0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2958713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2958714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2959056	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2959065	0.84[EUR][1000 genomes]
rs2959066	0.91[AFR][1000 genomes]
rs2959068	0.86[ASW][hapmap]
rs2959070	0.81[CEU][hapmap]
rs2959075	0.88[CEU][hapmap]
rs2959077	0.83[EUR][1000 genomes]
rs2959079	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2959081	0.93[ASW][hapmap];0.96[CEU][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs34662040	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910863	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4910864	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61188043	0.87[AFR][1000 genomes]
rs7102508	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7116520	0.89[AFR][1000 genomes]
rs7120938	0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs747883	0.91[AFR][1000 genomes]
rs7938196	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7945639	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2923944	RRM1	cis	Artery Tibial	GTEx
rs2923944	BRSK2	cis	cerebellum	SCAN
rs2923944	CTSD	cis	cerebellum	SCAN
rs2923944	OR51A4	cis	parietal	SCAN
rs2923944	RRM1	cis	Nerve Tibial	GTEx
rs2923944	STIM1	cis	parietal	SCAN
rs2923944	OR52B4	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:3962000-3971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:3962000-3973400	Weak transcription	Ovary	ovary
6	chr11:3963000-3973200	Enhancers	Primary B cells from peripheral blood	blood
7	chr11:3964400-3971600	Weak transcription	A549	lung
8	chr11:3964400-3972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:3964400-3972400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:3965800-3972000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:3966000-3972200	Weak transcription	Pancreas	Pancrea
12	chr11:3967000-3972600	Weak transcription	Fetal Intestine Small	intestine
13	chr11:3967400-3971200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr11:3967400-3971400	Enhancers	Fetal Heart	heart
15	chr11:3967800-3971200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:3968000-3972200	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:3968200-3972000	Weak transcription	Stomach Mucosa	stomach
18	chr11:3968200-3974600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:3968200-3980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:3968600-3971200	Flanking Active TSS	Dnd41	blood
21	chr11:3968600-3971800	Weak transcription	Osteobl	bone
22	chr11:3968600-3972200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:3968600-3972200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:3968600-3972200	Weak transcription	Brain Angular Gyrus	brain
25	chr11:3968800-3972000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:3968800-3974600	Weak transcription	HMEC	breast
27	chr11:3969000-3971400	Weak transcription	Spleen	Spleen
28	chr11:3969000-3971600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:3969000-3971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:3969000-3971800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:3969000-3971800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:3969000-3972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:3969000-3972200	Weak transcription	Right Atrium	heart
34	chr11:3969000-3972400	Weak transcription	Placenta	Placenta
35	chr11:3969000-3973200	Enhancers	Primary B cells from cord blood	blood
36	chr11:3969000-3974000	Weak transcription	Gastric	stomach
37	chr11:3969000-3974200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:3969000-3974600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:3969000-3975400	Weak transcription	NHDF-Ad	bronchial
40	chr11:3969000-3980400	Weak transcription	NHLF	lung
41	chr11:3969200-3971200	Weak transcription	HepG2	liver
42	chr11:3969200-3971800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:3969200-3972000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:3969200-3972000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:3969200-3972000	Weak transcription	Fetal Stomach	stomach
46	chr11:3969200-3972200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:3969400-3971800	Weak transcription	Brain Anterior Caudate	brain
48	chr11:3969400-3971800	Weak transcription	Left Ventricle	heart
49	chr11:3969400-3971800	Weak transcription	Right Ventricle	heart
50	chr11:3969400-3972000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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