Variant report

Variant	rs7174260
Chromosome Location	chr15:44044186-44044187
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	GATA3	chr15:44043772-44044247	MCF-7	breast:	n/a	chr15:44043996-44044017
2	CTCF	chr15:44043915-44044202	K562	blood:	n/a	chr15:44044012-44044033
3	POLR2A	chr15:44044077-44044479	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr15:44044061-44044583	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr15:44043515-44044262	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:44044154-44044524	HepG2	liver:	n/a	n/a
7	STAT3	chr15:44044082-44044258	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44036863..44039388-chr15:44043033..44046484,4	MCF-7	breast:

Variant related genes	Relation type
CATSPER2P1	TF binding region
ENSG00000167004	Chromatin interaction
ENSG00000205771	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs17795279	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs2412821	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2918947	0.82[EUR][1000 genomes]
rs2930529	0.93[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3102448	0.87[EUR][1000 genomes]
rs3110081	0.85[EUR][1000 genomes]
rs35822148	0.88[EUR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3986209	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs514311	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs541871	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs62018940	0.90[EUR][1000 genomes]
rs62018944	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7178230	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap]
rs8038068	1.00[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7174260	ZSCAN29	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44039200-44049400	Weak transcription	Spleen	Spleen
2	chr15:44039600-44052000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:44039600-44055400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:44039800-44048800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:44040200-44048200	Weak transcription	Fetal Kidney	kidney
6	chr15:44040200-44049200	Weak transcription	Esophagus	oesophagus
7	chr15:44040200-44056000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:44040200-44062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:44040400-44046000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:44040400-44046400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:44040600-44045800	Weak transcription	Fetal Brain Female	brain
12	chr15:44040600-44046800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:44040800-44055600	Weak transcription	Psoas Muscle	Psoas
14	chr15:44040800-44055800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:44041000-44044200	Enhancers	Stomach Mucosa	stomach
16	chr15:44041000-44045600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:44041000-44047000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:44041000-44068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:44042000-44066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:44042000-44066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:44042000-44067000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:44042200-44044200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:44042200-44044200	Weak transcription	A549	lung
24	chr15:44042200-44044400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:44042200-44044600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr15:44042200-44045000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:44042200-44045000	Weak transcription	Pancreas	Pancrea
28	chr15:44042200-44046000	Weak transcription	Colonic Mucosa	Colon
29	chr15:44042200-44046600	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:44042200-44049600	Weak transcription	Gastric	stomach
31	chr15:44042200-44055400	Weak transcription	Aorta	Aorta
32	chr15:44042200-44067000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:44042400-44045000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:44042400-44045000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:44042400-44046600	Weak transcription	Ovary	ovary
36	chr15:44042400-44049400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:44042600-44044600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr15:44042600-44045000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:44042600-44045000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:44042600-44045000	Weak transcription	Right Atrium	heart
41	chr15:44042600-44045200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:44042600-44045200	Weak transcription	Lung	lung
43	chr15:44042600-44045800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:44042600-44045800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:44042600-44046000	Weak transcription	Fetal Lung	lung
46	chr15:44042600-44046600	Weak transcription	Right Ventricle	heart
47	chr15:44042600-44048400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:44042600-44049400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:44042600-44053400	Weak transcription	Fetal Brain Male	brain
50	chr15:44042600-44066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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