Variant report

Variant	rs10037940
Chromosome Location	chr5:94049108-94049109
allele	C/T
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	chr5:94039956-94052296	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:94048115-94052802	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:94039895-94052973	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94041697..94043970-chr5:94047357..94049354,2	K562	blood:

Variant related genes	Relation type
MCTP1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10039102	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10039797	0.89[EUR][1000 genomes]
rs10052066	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs10062402	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10072894	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes]
rs10078522	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1031389	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs10476614	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1124667	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]
rs11948061	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]
rs12189060	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs1451734	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1549179	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2112448	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2112449	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2112450	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2636	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2638	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs306574	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs306578	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs306580	0.88[ASW][hapmap];0.91[GIH][hapmap]
rs421521	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs432449	0.85[GIH][hapmap]
rs6556849	0.96[EUR][1000 genomes]
rs747880	0.96[EUR][1000 genomes]
rs755899	0.94[EUR][1000 genomes]
rs755901	0.83[EUR][1000 genomes]
rs7709494	0.96[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes]
rs7735924	0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10037940	MCTP1	cis	uninvolved skin	skin_eQTL
rs10037940	ELL2	cis	parietal	SCAN
rs10037940	MCTP1	cis	multi-tissue	Pritchard
rs10037940	MCTP1	cis	lesional skin	skin_eQTL
rs10037940	MCTP1	cis	Cerebellum	GTEx
rs10037940	MCTP1	cis	normal skin	skin_eQTL
rs10037940	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs10037940	MCTP1	cis	lymphoblastoid	seeQTL
rs10037940	C5orf36	cis	cerebellum	SCAN
rs10037940	C5orf36	cis	parietal	SCAN
rs10037940	ANKRD32	cis	parietal	SCAN
rs10037940	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10037940	MCTP1	cis	Temporal Cortex	GTEx
rs10037940	ANKRD32	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
2	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
8	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
10	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:94025800-94050800	Weak transcription	K562	blood
13	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
20	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
22	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
23	chr5:94029800-94050000	Weak transcription	Osteobl	bone
24	chr5:94030200-94051400	Weak transcription	HSMM	muscle
25	chr5:94031000-94050000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:94031000-94050000	Weak transcription	Liver	Liver
27	chr5:94031000-94051200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:94031000-94052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:94031200-94050600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:94034200-94051400	Weak transcription	Pancreas	Pancrea
31	chr5:94035400-94052000	Weak transcription	Fetal Kidney	kidney
32	chr5:94037400-94051000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:94039000-94050800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:94039000-94064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:94039800-94052000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:94040200-94050600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:94040800-94052400	Weak transcription	Fetal Stomach	stomach
38	chr5:94041400-94051400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:94041600-94050600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:94041800-94051600	Weak transcription	Brain Anterior Caudate	brain
41	chr5:94042800-94049400	Strong transcription	HUVEC	blood vessel
42	chr5:94042800-94050000	Weak transcription	NHEK	skin
43	chr5:94043200-94050600	Strong transcription	Hela-S3	cervix
44	chr5:94043200-94051000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:94043400-94049400	Strong transcription	Dnd41	blood
46	chr5:94043400-94050600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:94043600-94051000	Strong transcription	Fetal Thymus	thymus
48	chr5:94043600-94053000	Weak transcription	GM12878-XiMat	blood
49	chr5:94043800-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr5:94044200-94049400	Strong transcription	Primary T cells from cord blood	blood

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