Variant report

Variant	rs2930531
Chromosome Location	chr15:44121570-44121571
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	ZNF384	chr15:44121507-44121705	GM12878	blood:	n/a	n/a
2	ZNF384	chr15:44121516-44121775	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44112442..44117510-chr15:44119138..44122295,7	K562	blood:
2	chr15:44069535..44071546-chr15:44121080..44123545,2	K562	blood:
3	chr15:44116010..44118806-chr15:44119254..44122105,3	K562	blood:

Variant related genes	Relation type
MFAP1	TF binding region
ENSG00000140259	Chromatin interaction
ENSG00000128886	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2412821	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2918943	1.00[YRI][hapmap]
rs2918947	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2930529	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3102448	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35267287	0.90[AFR][1000 genomes]
rs35822148	0.89[EUR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3986209	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs495880	0.93[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018940	0.84[EUR][1000 genomes]
rs62018944	0.81[EUR][1000 genomes]
rs6493090	0.86[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs654276	0.93[ASW][hapmap];0.94[CEU][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs678084	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174241	0.87[GIH][hapmap]
rs7174260	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7178230	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers 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	90 gene(s)	inside rSNPs	diseases
5	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
7	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
8	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
10	nsv511550	chr15:44120559-44148142	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2930531	WDR76	cis	parietal	SCAN
rs2930531	TUBGCP4	cis	parietal	SCAN
rs2930531	ZSCAN29	cis	multi-tissue	Pritchard
rs2930531	STRC	cis	multi-tissue	Pritchard
rs2930531	ZNF690	cis	multi-tissue	Pritchard
rs2930531	TGM5	cis	lymphoblastoid	seeQTL
rs2930531	MAPKBP1	cis	parietal	SCAN
rs2930531	ZSCAN29	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44117400-44150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:44119600-44121800	Weak transcription	Placenta	Placenta
3	chr15:44119600-44123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:44119600-44127200	Weak transcription	Left Ventricle	heart
5	chr15:44119600-44127200	Weak transcription	Ovary	ovary
6	chr15:44119600-44127600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:44119600-44127600	Weak transcription	Gastric	stomach
8	chr15:44119600-44130600	Weak transcription	Brain Anterior Caudate	brain
9	chr15:44119600-44134400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:44119600-44135200	Weak transcription	Lung	lung
11	chr15:44119600-44142000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:44119600-44143200	Weak transcription	Aorta	Aorta
13	chr15:44119600-44143400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:44119600-44150600	Weak transcription	Esophagus	oesophagus
15	chr15:44119600-44151000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:44119600-44156400	Weak transcription	Pancreas	Pancrea
17	chr15:44119600-44166000	Weak transcription	Spleen	Spleen
18	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
19	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
21	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr15:44119800-44121600	Enhancers	Fetal Heart	heart
23	chr15:44119800-44122800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:44119800-44127600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:44119800-44144400	Weak transcription	Right Ventricle	heart
26	chr15:44119800-44166400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:44120200-44122400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:44120200-44124400	Weak transcription	Fetal Intestine Small	intestine
29	chr15:44120200-44126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:44120200-44126800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:44120200-44126800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:44120200-44127800	Weak transcription	Primary B cells from cord blood	blood
33	chr15:44120200-44128000	Weak transcription	Adipose Nuclei	Adipose
34	chr15:44120200-44150800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:44120400-44121600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr15:44120400-44121600	Transcr. at gene 5' and 3'	K562	blood
37	chr15:44120400-44123800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:44120400-44125400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:44120400-44127000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:44120400-44128000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:44120400-44143000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:44120600-44121600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr15:44120600-44121800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:44120600-44122200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:44120600-44122400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:44120600-44126800	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:44120600-44127000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:44120600-44127200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:44120600-44127200	Weak transcription	Thymus	Thymus
50	chr15:44120600-44127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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