Variant report

Variant	rs541871
Chromosome Location	chr15:44160854-44160855
allele	C/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	EBF1	chr15:44160588-44161014	GM12878	blood:	n/a	chr15:44160816-44160825 chr15:44160814-44160827 chr15:44160815-44160825 chr15:44160815-44160826 chr15:44160816-44160825
2	POLR2A	chr15:44160698-44161006	H1-neurons	neurons:	n/a	n/a
3	EBF1	chr15:44160690-44160956	GM12878	blood:	n/a	chr15:44160816-44160825 chr15:44160814-44160827 chr15:44160815-44160825 chr15:44160815-44160826 chr15:44160816-44160825
4	EBF1	chr15:44160650-44160953	GM12878	blood:	n/a	chr15:44160816-44160825 chr15:44160814-44160827 chr15:44160815-44160825 chr15:44160815-44160826 chr15:44160816-44160825
5	POLR2A	chr15:44160632-44160985	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr15:44160481-44160955	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr15:44160818-44160926	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44149483..44153961-chr15:44160698..44164757,7	K562	blood:
2	chr15:44158321..44161278-chr15:44164500..44166500,2	K562	blood:
3	chr15:44152030..44153831-chr15:44160698..44163562,2	K562	blood:
4	chr15:44158756..44161490-chr15:44163226..44166726,5	K562	blood:
5	chr15:44153055..44155355-chr15:44158587..44161206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200391	TF binding region
ENSG00000092470	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10163069	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11070411	0.94[CEU][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs12443084	0.94[CEU][hapmap]
rs2412821	0.93[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2729494	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28410121	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2918943	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2918947	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2930529	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930530	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930531	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3102448	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35267287	0.93[AFR][1000 genomes]
rs3862143	0.94[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs3986209	0.83[EUR][1000 genomes]
rs4644832	0.95[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4923964	0.95[CEU][hapmap]
rs4923965	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs495880	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs514311	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs528764	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493090	0.94[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs654276	0.89[CEU][hapmap];0.87[YRI][hapmap]
rs678084	0.94[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7174260	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7178230	0.83[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	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
2	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
3	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
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs541871	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44166000	Weak transcription	Spleen	Spleen
2	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
3	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
5	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:44119800-44166400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:44120600-44161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:44120600-44164600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:44120600-44164600	Weak transcription	NHEK	skin
10	chr15:44120600-44165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:44124000-44166000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:44128200-44167800	Weak transcription	Ovary	ovary
14	chr15:44128600-44167800	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:44129200-44161200	Weak transcription	Brain Substantia Nigra	brain
16	chr15:44131200-44167600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:44133000-44166000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:44142200-44163800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:44142200-44164600	Weak transcription	Brain Angular Gyrus	brain
20	chr15:44144800-44181000	Weak transcription	HepG2	liver
21	chr15:44146600-44165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:44146600-44165800	Weak transcription	Osteobl	bone
23	chr15:44146800-44181600	Weak transcription	Gastric	stomach
24	chr15:44147600-44172000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:44148200-44166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:44149600-44166200	Weak transcription	A549	lung
27	chr15:44150600-44174600	Strong transcription	Dnd41	blood
28	chr15:44151200-44161600	Weak transcription	Fetal Heart	heart
29	chr15:44151600-44171200	Weak transcription	Placenta	Placenta
30	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:44152000-44161000	Weak transcription	NH-A	brain
32	chr15:44152000-44172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:44152200-44161400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:44152200-44166400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:44152400-44161200	Weak transcription	Left Ventricle	heart
36	chr15:44152400-44164600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:44152600-44161400	Weak transcription	HMEC	breast
38	chr15:44152600-44164400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:44152600-44166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:44152600-44167800	Weak transcription	Aorta	Aorta
41	chr15:44152600-44168000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:44152600-44168600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:44152600-44169600	Weak transcription	Lung	lung
44	chr15:44152600-44180800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:44152800-44166200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:44153000-44161200	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:44153600-44163400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:44153800-44166000	Weak transcription	NHLF	lung
49	chr15:44153800-44166200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:44153800-44172000	Weak transcription	Stomach Smooth Muscle	stomach

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