Variant report

Variant	rs727175
Chromosome Location	chr7:102471780-102471781
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	TCF12	chr7:102469702-102472055	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102470809..102472496-chr7:102473289..102475572,2	MCF-7	breast:
2	chr7:102471265..102473661-chr7:102474795..102476825,2	K562	blood:

Variant related genes	Relation type
RNU6-1136P	TF binding region
ENSG00000252643	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10487281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11496066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113233	0.91[AFR][1000 genomes]
rs12113759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs17135875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17474893	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215040	0.82[TSI][hapmap]
rs2411061	1.00[CHB][hapmap]
rs3893651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377880	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4398822	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55681588	1.00[ASN][1000 genomes]
rs55781834	1.00[ASN][1000 genomes]
rs56146438	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56186316	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56314487	1.00[ASN][1000 genomes]
rs56692051	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6955064	1.00[ASN][1000 genomes]
rs6964296	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs6968036	1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs73192015	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192019	1.00[ASN][1000 genomes]
rs7779854	1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs7781557	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790451	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv608059	chr7:102470455-102504773	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs727175	CUX1	cis	cerebellum	SCAN
rs727175	MEPCE	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102421600-102475600	Weak transcription	Fetal Thymus	thymus
2	chr7:102422000-102474800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:102447400-102477200	Weak transcription	Psoas Muscle	Psoas
5	chr7:102447800-102473000	Weak transcription	Placenta	Placenta
6	chr7:102448000-102479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:102448400-102471800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:102450000-102475000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:102450200-102475600	Weak transcription	Esophagus	oesophagus
10	chr7:102452000-102480000	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:102452200-102472800	Weak transcription	HSMMtube	muscle
12	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:102454400-102475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:102454600-102475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:102454600-102475600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:102454800-102473200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:102455000-102475000	Weak transcription	NHLF	lung
18	chr7:102455000-102475000	Weak transcription	Osteobl	bone
19	chr7:102455200-102472800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:102455600-102473200	Weak transcription	HSMM	muscle
21	chr7:102459800-102481800	Weak transcription	Brain Substantia Nigra	brain
22	chr7:102460000-102474800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:102460000-102475000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:102460200-102475200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:102460400-102474600	Weak transcription	HUVEC	blood vessel
26	chr7:102460400-102477000	Weak transcription	Stomach Mucosa	stomach
27	chr7:102460400-102480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:102460800-102480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:102463200-102475000	Weak transcription	A549	lung
30	chr7:102466200-102473800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:102466400-102472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:102466400-102475000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:102467400-102472000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:102467600-102473000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:102468000-102474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:102468000-102475000	Weak transcription	HMEC	breast
37	chr7:102468000-102484600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:102468200-102481000	Weak transcription	Brain Germinal Matrix	brain
39	chr7:102468800-102471800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr7:102469000-102473400	Strong transcription	K562	blood
41	chr7:102469200-102472000	Enhancers	Fetal Brain Male	brain
42	chr7:102469600-102471800	Strong transcription	Left Ventricle	heart
43	chr7:102469800-102477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:102469800-102478400	Weak transcription	Fetal Intestine Small	intestine
45	chr7:102469800-102478800	Weak transcription	Primary B cells from cord blood	blood
46	chr7:102470000-102472800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:102470000-102475600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:102470000-102477600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:102470000-102478000	Weak transcription	HepG2	liver
50	chr7:102470000-102479000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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