Variant report

Variant	rs7178546
Chromosome Location	chr15:93197424-93197425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93197350-93197944	HUVEC	blood vessel:	n/a	n/a
2	CHD1	chr15:93197362-93197533	GM12878	blood:	n/a	n/a
3	MXI1	chr15:93197423-93197656	GM12878	blood:	n/a	n/a
4	CTCF	chr15:93197369-93197752	GM12878	blood:	n/a	n/a
5	NR3C1	chr15:93197284-93197731	A549	lung:	n/a	chr15:93197535-93197550
6	RAD21	chr15:93197418-93197673	GM12878	blood:	n/a	n/a
7	ATF2	chr15:93197126-93197783	GM12878	blood:	n/a	n/a
8	MYC	chr15:93197376-93197440	HUVEC	blood vessel:	n/a	n/a
9	RAD21	chr15:93197266-93197818	MCF-7	breast:	n/a	n/a
10	CTCF	chr15:93197400-93197550	GM12865	blood:	n/a	n/a
11	FOXA1	chr15:93197343-93197724	T-47D	breast:	n/a	n/a
12	CTCF	chr15:93197343-93197833	MCF-7	breast:	n/a	n/a
13	POLR2A	chr15:93197233-93198042	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr15:93197033-93197836	GM12878	blood:	n/a	n/a
15	STAT1	chr15:93197276-93197727	GM12878	blood:	n/a	n/a
16	ZNF143	chr15:93197387-93197685	GM12878	blood:	n/a	n/a
17	CTCF	chr15:93197400-93197550	HA-sp	spinal cord:	n/a	n/a
18	FOXA2	chr15:93197345-93197864	A549	lung:	n/a	n/a
19	MTA3	chr15:93197229-93197694	GM12878	blood:	n/a	n/a
20	RUNX3	chr15:93196932-93197690	GM12878	blood:	n/a	n/a
21	FOXA1	chr15:93197354-93197655	HepG2	liver:	n/a	n/a
22	TBL1XR1	chr15:93197411-93197746	GM12878	blood:	n/a	n/a
23	CUX1	chr15:93197228-93197657	GM12878	blood:	n/a	n/a
24	TCF12	chr15:93197157-93197886	A549	lung:	n/a	chr15:93197172-93197181 chr15:93197377-93197384
25	WRNIP1	chr15:93197261-93197779	GM12878	blood:	n/a	n/a
26	RAD21	chr15:93197201-93197869	MCF-7	breast:	n/a	n/a
27	POLR2A	chr15:93197333-93197824	H1-neurons	neurons:	n/a	n/a
28	CTCF	chr15:93197420-93197570	HRE	kidney:	n/a	n/a
29	FOXA2	chr15:93197351-93197815	A549	lung:	n/a	n/a
30	FOXA1	chr15:93197418-93197662	T-47D	breast:	n/a	n/a
31	FOXP2	chr15:93197414-93197687	PFSK-1	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93145840..93149737-chr15:93196292..93199149,3	MCF-7	breast:
2	chr15:93197096..93198076-chr15:93225951..93227103,4	MCF-7	breast:
3	chr15:93196488..93198404-chr17:67442282..67443797,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM174B	TF binding region
ENSG00000271763	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12443091	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254142	0.92[EUR][1000 genomes]
rs2453901	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.90[EUR][1000 genomes]
rs285755	0.91[EUR][1000 genomes]
rs285757	0.91[EUR][1000 genomes]
rs285758	0.91[EUR][1000 genomes]
rs285766	0.83[EUR][1000 genomes]
rs285772	0.93[EUR][1000 genomes]
rs366789	0.85[EUR][1000 genomes]
rs373481	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496969	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7178546	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93182000-93197800	Weak transcription	Small Intestine	intestine
2	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:93193800-93199000	Enhancers	Fetal Heart	heart
4	chr15:93194200-93198200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:93194400-93198400	Weak transcription	Brain Anterior Caudate	brain
6	chr15:93194600-93197600	Weak transcription	Fetal Brain Female	brain
7	chr15:93194600-93198400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:93195000-93197600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr15:93195400-93197600	Flanking Active TSS	Pancreas	Pancrea
11	chr15:93195400-93197600	Enhancers	Right Ventricle	heart
12	chr15:93195600-93197600	Enhancers	Fetal Intestine Large	intestine
13	chr15:93195600-93197600	Genic enhancers	Fetal Muscle Leg	muscle
14	chr15:93195600-93198000	Enhancers	Right Atrium	heart
15	chr15:93195800-93197600	Enhancers	Brain Angular Gyrus	brain
16	chr15:93195800-93198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:93196200-93198000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:93196200-93198200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:93196600-93197600	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr15:93196600-93199200	Enhancers	Fetal Brain Male	brain
21	chr15:93196800-93197600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr15:93196800-93197800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr15:93196800-93197800	Enhancers	Left Ventricle	heart
24	chr15:93196800-93197800	Enhancers	Lung	lung
25	chr15:93196800-93198000	Enhancers	Colon Smooth Muscle	Colon
26	chr15:93196800-93198000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:93196800-93198200	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr15:93196800-93198400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:93197000-93197600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:93197000-93197600	Enhancers	Brain Hippocampus Middle	brain
31	chr15:93197000-93197800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:93197000-93197800	Enhancers	Ovary	ovary
33	chr15:93197000-93197800	Flanking Active TSS	Stomach Mucosa	stomach
34	chr15:93197000-93198000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:93197000-93198000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:93197000-93198200	Enhancers	Fetal Thymus	thymus
37	chr15:93197000-93198400	Enhancers	Esophagus	oesophagus
38	chr15:93197000-93199600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:93197200-93197600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr15:93197200-93197600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr15:93197200-93197600	Flanking Active TSS	Gastric	stomach
42	chr15:93197200-93197600	Flanking Active TSS	HSMM	muscle
43	chr15:93197200-93197800	Enhancers	Fetal Intestine Small	intestine
44	chr15:93197200-93197800	Flanking Active TSS	Fetal Kidney	kidney
45	chr15:93197200-93197800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr15:93197200-93198000	Enhancers	H9 Cell Line	embryonic stem cell
47	chr15:93197200-93198000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:93197200-93198000	Enhancers	Colonic Mucosa	Colon
49	chr15:93197200-93198200	Flanking Active TSS	HUVEC	blood vessel
50	chr15:93197200-93198400	Enhancers	Brain Substantia Nigra	brain

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