Variant report

Variant	rs1124667
Chromosome Location	chr5:94012979-94012980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:94012960-94013032	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:94011934-94013557	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:94011749-94013110	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ANKRD32	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10037940	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10039102	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10039797	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10052066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062402	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074178	0.84[AMR][1000 genomes]
rs10078522	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031389	0.93[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs10476614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948061	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	0.88[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]
rs1451734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112448	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2112449	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112450	0.82[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]
rs2636	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2638	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs306574	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs306578	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs306580	0.81[ASW][hapmap];0.89[GIH][hapmap]
rs395097	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs421521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs432449	0.83[GIH][hapmap]
rs6556849	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747880	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755899	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755901	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7709494	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735924	0.82[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[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	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1124667	C5orf36	cis	cerebellum	SCAN
rs1124667	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs1124667	MCTP1	cis	normal skin	skin_eQTL
rs1124667	MCTP1	cis	Cerebellum	GTEx
rs1124667	MCTP1	cis	lymphoblastoid	seeQTL
rs1124667	ANKRD32	cis	parietal	SCAN
rs1124667	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs1124667	MCTP1	cis	Temporal Cortex	GTEx
rs1124667	MCTP1	cis	lesional skin	skin_eQTL
rs1124667	MCTP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:105 , 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	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
5	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:93994400-94027600	Weak transcription	Liver	Liver
9	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
10	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
12	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
13	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:93995400-94024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:93995600-94024400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
19	chr5:93996000-94024000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
22	chr5:93996200-94026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:93996200-94029800	Weak transcription	Ovary	ovary
24	chr5:93996600-94019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:93996600-94023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:93996600-94048400	Weak transcription	Lung	lung
28	chr5:93996800-94013800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:93996800-94036200	Weak transcription	Gastric	stomach
30	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
31	chr5:94001000-94030000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:94001200-94017600	Weak transcription	Primary B cells from cord blood	blood
33	chr5:94001200-94022400	Weak transcription	Fetal Stomach	stomach
34	chr5:94001200-94023000	Weak transcription	Adipose Nuclei	Adipose
35	chr5:94001400-94016800	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:94001600-94024200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:94001800-94022400	Weak transcription	Thymus	Thymus
38	chr5:94001800-94027600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:94002000-94022200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:94003800-94023000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:94004000-94014600	Weak transcription	Primary T cells from cord blood	blood
42	chr5:94004000-94022600	Weak transcription	Fetal Intestine Large	intestine
43	chr5:94004400-94016800	Weak transcription	Fetal Intestine Small	intestine
44	chr5:94004600-94022400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:94006800-94014400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:94007200-94025800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:94008800-94027600	Weak transcription	Osteobl	bone
49	chr5:94009000-94019400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:94009000-94024200	Weak transcription	Primary hematopoietic stem cells	blood

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