Variant report

Variant	rs2930530
Chromosome Location	chr15:44115466-44115467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:44115372-44115739	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44089939..44094924-chr15:44115270..44119372,7	MCF-7	breast:
2	chr15:44089858..44095024-chr15:44113933..44120718,10	MCF-7	breast:
3	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
4	chr15:44082407..44088245-chr15:44114276..44118984,12	MCF-7	breast:
5	chr15:44066351..44069155-chr15:44115292..44116970,2	MCF-7	breast:
6	chr15:44036424..44040091-chr15:44115436..44119319,5	K562	blood:
7	chr15:44068154..44070774-chr15:44115060..44118766,3	K562	blood:
8	chr15:44112442..44117510-chr15:44119138..44122295,7	K562	blood:

No data

Variant related genes	Relation type
WDR76	TF binding region
ENSG00000140264	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000092470	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000167004	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10163069	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12443084	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.84[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];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs2918947	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2930529	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930531	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	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3110081	0.81[EUR][1000 genomes]
rs35822148	0.92[EUR][1000 genomes]
rs3844075	0.96[YRI][hapmap]
rs3862143	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3986209	0.94[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018940	0.85[EUR][1000 genomes]
rs62018944	0.82[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7174241	0.84[GIH][hapmap]
rs7174260	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7178230	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2930530	TUBGCP4	cis	parietal	SCAN
rs2930530	ZSCAN29	cis	multi-tissue	Pritchard
rs2930530	ZSCAN29	cis	lymphoblastoid	seeQTL
rs2930530	MAPKBP1	cis	parietal	SCAN
rs2930530	TGM5	cis	lymphoblastoid	seeQTL
rs2930530	WDR76	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44093600-44116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44093600-44116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44093800-44115800	Weak transcription	Right Atrium	heart
4	chr15:44105000-44115800	Weak transcription	Psoas Muscle	Psoas
5	chr15:44106800-44115600	Weak transcription	Right Ventricle	heart
6	chr15:44107200-44116000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:44107400-44115600	Weak transcription	Fetal Heart	heart
8	chr15:44107800-44115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:44107800-44115800	Weak transcription	Gastric	stomach
10	chr15:44108000-44115800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:44109800-44115600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:44109800-44115800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:44109800-44115800	Weak transcription	HSMMtube	muscle
14	chr15:44109800-44116000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:44110000-44115600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:44110000-44115600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:44110000-44115600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:44110000-44115600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:44110000-44115600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:44110000-44115600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:44110000-44115600	Weak transcription	Fetal Kidney	kidney
22	chr15:44110000-44115600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:44110000-44115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:44110000-44115800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:44110000-44115800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:44110000-44115800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:44110000-44115800	Weak transcription	A549	lung
28	chr15:44110000-44115800	Weak transcription	NH-A	brain
29	chr15:44110000-44115800	Weak transcription	NHDF-Ad	bronchial
30	chr15:44110200-44115600	Weak transcription	Colonic Mucosa	Colon
31	chr15:44110200-44115600	Weak transcription	HSMM	muscle
32	chr15:44110200-44115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:44110200-44115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:44110600-44115600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:44110600-44115800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:44111200-44115600	Weak transcription	Osteobl	bone
37	chr15:44111600-44115800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:44112400-44115800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:44112400-44115800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:44112600-44115800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:44112600-44115800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:44112600-44116400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:44112800-44116400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr15:44113000-44115600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr15:44113200-44115600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:44113400-44115600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:44113800-44115800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:44113800-44115800	Enhancers	HepG2	liver
49	chr15:44113800-44115800	Enhancers	HUVEC	blood vessel
50	chr15:44114000-44115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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