Variant report

Variant	rs7175269
Chromosome Location	chr15:41241567-41241568
allele	C/T
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	BHLHE40	chr15:41241393-41241638	HepG2	liver:	n/a	chr15:41241449-41241470
2	BHLHE40	chr15:41241280-41241651	K562	blood:	n/a	chr15:41241449-41241470
3	MAX	chr15:41241172-41241614	H1-hESC	embryonic stem cell:	n/a	chr15:41241444-41241453 chr15:41241444-41241454 chr15:41241457-41241473 chr15:41241445-41241452 chr15:41241443-41241454 chr15:41241440-41241455 chr15:41241446-41241462
4	MAX	chr15:41241232-41241667	K562	blood:	n/a	chr15:41241444-41241453 chr15:41241444-41241454 chr15:41241457-41241473 chr15:41241445-41241452 chr15:41241443-41241454 chr15:41241440-41241455 chr15:41241446-41241462
5	MAX	chr15:41241205-41241715	H1-hESC	embryonic stem cell:	n/a	chr15:41241444-41241453 chr15:41241444-41241454 chr15:41241457-41241473 chr15:41241445-41241452 chr15:41241443-41241454 chr15:41241440-41241455 chr15:41241446-41241462
6	E2F6	chr15:41241046-41241819	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41164626..41166627-chr15:41240824..41242386,2	MCF-7	breast:
2	chr15:41219948..41223850-chr15:41241031..41249080,13	K562	blood:

Variant related genes	Relation type
CHAC1	TF binding region
ISCA1P4	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11070312	0.90[ASN][1000 genomes]
rs11557249	1.00[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs11632640	0.91[ASN][1000 genomes]
rs11634736	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11853377	0.91[EUR][1000 genomes]
rs11854054	0.95[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs11857572	0.88[EUR][1000 genomes]
rs28473405	0.82[TSI][hapmap]
rs28575174	0.91[EUR][1000 genomes]
rs2925343	0.85[MEX][hapmap];0.89[TSI][hapmap]
rs4924519	0.83[ASN][1000 genomes]
rs6492971	0.86[CHD][hapmap]
rs745299	0.96[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.89[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7175269	C15orf62	cis	parietal	SCAN
rs7175269	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7175269	GPR176	cis	cerebellum	SCAN
rs7175269	NDUFAF1	cis	parietal	SCAN
rs7175269	SPINT1	cis	cerebellum	SCAN
rs7175269	RASGRP1	cis	parietal	SCAN
rs7175269	GPR176	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41235400-41244600	Weak transcription	NHLF	lung
2	chr15:41235800-41244800	Weak transcription	Esophagus	oesophagus
3	chr15:41236200-41244600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41238600-41244400	Weak transcription	GM12878-XiMat	blood
5	chr15:41240600-41242200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr15:41240800-41241600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr15:41240800-41241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr15:41240800-41242600	Enhancers	K562	blood
9	chr15:41241000-41241600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41241000-41241600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:41241000-41242000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:41241000-41242000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr15:41241000-41242000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:41241000-41242000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr15:41241000-41242000	Enhancers	Left Ventricle	heart
16	chr15:41241000-41242200	Enhancers	Lung	lung
17	chr15:41241200-41241800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:41241200-41242000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:41241200-41242200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:41241200-41242200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:41241200-41242400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:41241200-41244000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:41241200-41244200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:41241400-41241800	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:41241400-41241800	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr15:41241400-41241800	Enhancers	Fetal Thymus	thymus
27	chr15:41241400-41241800	Enhancers	Gastric	stomach
28	chr15:41241400-41242000	Enhancers	Pancreas	Pancrea
29	chr15:41241400-41242000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr15:41241400-41242200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr15:41241400-41242200	Enhancers	Stomach Mucosa	stomach
32	chr15:41241400-41242400	Enhancers	Adipose Nuclei	Adipose
33	chr15:41241400-41242400	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:41241400-41242400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:41241400-41242600	Enhancers	Fetal Intestine Small	intestine
36	chr15:41241400-41242600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr15:41241400-41243000	Enhancers	Liver	Liver
38	chr15:41241400-41244400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:41241400-41244600	Weak transcription	Brain Cingulate Gyrus	brain

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