Variant report

Variant	rs11948061
Chromosome Location	chr5:93995589-93995590
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	chr5:93954192..93956336-chr5:93995387..93997167,2	K562	blood:

Variant related genes	Relation type
ENSG00000133302	Chromatin interaction
ENSG00000185261	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10037940	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10039102	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10039797	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10052066	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062402	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072894	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074178	0.82[AMR][1000 genomes]
rs10078522	0.91[CEU][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031389	0.80[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs10476614	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124667	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451734	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549179	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112448	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2112449	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112450	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2638	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs306580	0.82[GIH][hapmap]
rs395097	0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs421521	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs432449	0.89[GIH][hapmap]
rs449798	0.90[YRI][hapmap]
rs6556849	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747880	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755899	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755901	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7709494	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735924	0.85[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.95[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	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv882386	chr5:93973177-94008969	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11948061	MCTP1	cis	Temporal Cortex	GTEx
rs11948061	MCTP1	cis	normal skin	skin_eQTL
rs11948061	MCTP1	cis	Cerebellum	GTEx
rs11948061	ANKRD32	cis	multi-tissue	Pritchard
rs11948061	MCTP1	cis	lymphoblastoid	seeQTL
rs11948061	ANKRD32	cis	cerebellum	SCAN
rs11948061	C5orf36	cis	cerebellum	SCAN
rs11948061	MCTP1	cis	uninvolved skin	skin_eQTL
rs11948061	LIX1	cis	parietal	SCAN
rs11948061	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs11948061	MCTP1	cis	multi-tissue	Pritchard
rs11948061	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs11948061	ANKRD32	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955800-94027600	Weak transcription	NH-A	brain
2	chr5:93963800-93995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:93969400-94008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:93973800-94004200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
6	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
8	chr5:93988400-93996200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:93988600-93997800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:93988800-93995800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:93989000-93995600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:93990200-93995800	ZNF genes & repeats	A549	lung
13	chr5:93990600-93995600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:93990600-93995800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr5:93990600-93996200	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr5:93990600-94008200	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:93992800-93998000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:93993000-93995600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr5:93993000-93995600	ZNF genes & repeats	Fetal Lung	lung
21	chr5:93993200-93995600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
22	chr5:93993600-93996000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:93994000-93999000	Weak transcription	Osteobl	bone
24	chr5:93994200-93999600	Weak transcription	Adipose Nuclei	Adipose
25	chr5:93994200-93999800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:93994200-94010200	Weak transcription	NHEK	skin
27	chr5:93994200-94012000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
29	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:93994400-93995600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:93994400-93997600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:93994400-93998600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:93994400-94000200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:93994400-94000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:93994400-94006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:93994400-94012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:93994400-94027600	Weak transcription	Liver	Liver
40	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
41	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
43	chr5:93994600-93997000	Strong transcription	Dnd41	blood
44	chr5:93994600-93997200	Weak transcription	Colonic Mucosa	Colon
45	chr5:93994600-93997800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:93994600-93999800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr5:93994600-94000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:93994600-94007400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
50	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain

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