Variant report

Variant	rs7169404
Chromosome Location	chr15:40675443-40675444
allele	G/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	POLR2A	chr15:40674845-40675923	Hela-S3	cervix:	n/a	n/a
2	GABPA	chr15:40674704-40675741	K562	blood:	n/a	n/a
3	POLR2A	chr15:40675033-40675689	GM12878	blood:	n/a	n/a
4	HCFC1	chr15:40674786-40675548	K562	blood:	n/a	n/a
5	POLR2A	chr15:40674973-40675695	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:40674839-40675729	NB4	blood:	n/a	n/a
7	MAX	chr15:40674866-40675934	NB4	blood:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708
8	MAX	chr15:40674822-40675775	K562	blood:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708
9	SIN3AK20	chr15:40674760-40675716	MCF-7	breast:	n/a	n/a
10	EGR1	chr15:40674680-40675513	HCT-116	colon:	n/a	chr15:40675104-40675118
11	MXI1	chr15:40674975-40675818	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:40674949-40675655	MCF-7	breast:	n/a	n/a
13	MYC	chr15:40674993-40675920	MCF10A-Er-Src	breast:	n/a	chr15:40675694-40675704 chr15:40675693-40675708
14	YY1	chr15:40674640-40675575	A549	lung:	n/a	chr15:40675032-40675044
15	POLR2A	chr15:40674880-40675823	HL-60	blood:	n/a	n/a
16	POLR2A	chr15:40674991-40675560	GM19193	blood:	n/a	n/a
17	POLR2A	chr15:40674952-40676140	K562	blood:	n/a	n/a
18	POLR2A	chr15:40674859-40675737	ECC-1	luminal epithelium:	n/a	n/a
19	SMARCB1	chr15:40674830-40675723	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr15:40674903-40675465	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr15:40674846-40675878	K562	blood:	n/a	n/a
22	CREB1	chr15:40674728-40675622	HepG2	liver:	n/a	n/a
23	POLR2A	chr15:40674988-40675632	GM15510	blood:	n/a	n/a
24	TAF1	chr15:40674859-40675572	K562	blood:	n/a	n/a
25	GABPA	chr15:40674719-40675618	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr15:40674806-40675734	H1-neurons	neurons:	n/a	n/a
27	FOXM1	chr15:40674679-40675866	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr15:40674838-40676024	HepG2	liver:	n/a	n/a
29	MYBL2	chr15:40674761-40675508	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:40675365-40675681	Hela-S3	cervix:	n/a	n/a
31	RUNX3	chr15:40674853-40675607	GM12878	blood:	n/a	n/a
32	GABPA	chr15:40674692-40675708	SK-N-SH	brain:	n/a	n/a
33	HEY1	chr15:40674857-40675753	K562	blood:	n/a	n/a
34	ZC3H11A	chr15:40674872-40675679	K562	blood:	n/a	n/a
35	CHD2	chr15:40674973-40675540	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr15:40674666-40675641	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr15:40674910-40675918	K562	blood:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708
38	POLR2A	chr15:40674991-40675463	IMR90	lung:	n/a	n/a
39	POLR2A	chr15:40674799-40675451	H1-neurons	neurons:	n/a	n/a
40	GABPA	chr15:40674735-40675653	A549	lung:	n/a	n/a
41	NR2F2	chr15:40674782-40675530	K562	blood:	n/a	n/a
42	FOXM1	chr15:40674754-40675749	GM12878	blood:	n/a	n/a
43	BCLAF1	chr15:40674867-40675590	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:40674920-40675900	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr15:40674907-40675739	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr15:40674979-40675626	MCF-7	breast:	n/a	n/a
47	GABPA	chr15:40674807-40675636	K562	blood:	n/a	n/a
48	POLR2A	chr15:40674877-40675730	K562	blood:	n/a	n/a
49	SP1	chr15:40674859-40675456	A549	lung:	n/a	chr15:40675051-40675062
50	MAX	chr15:40674863-40675935	A549	lung:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708

No.	Distal block	Cell Line	Cell type
1	chr15:40674190..40678981-chr15:40695777..40699659,7	MCF-7	breast:
2	chr15:40675071..40677376-chr15:40697128..40699914,2	K562	blood:
3	chr15:40675097..40677864-chr15:40680611..40684131,5	K562	blood:
4	chr15:40660534..40665869-chr15:40673827..40676646,4	K562	blood:
5	chr15:40674973..40675561-chr6:80815881..80816507,2	Hela-S3	cervix:
6	chr15:40663732..40667062-chr15:40674726..40678158,3	MCF-7	breast:

Variant related genes	Relation type
KNSTRN	TF binding region
ENSG00000140323	Chromatin interaction
ENSG00000259714	Chromatin interaction
ENSG00000259368	Chromatin interaction
ENSG00000128944	Chromatin interaction
ENSG00000083123	Chromatin interaction
ENSG00000128928	Chromatin interaction
ENSG00000261374	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11557072	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858714	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905240	1.00[JPT][hapmap]
rs16970709	1.00[JPT][hapmap]
rs16970758	1.00[JPT][hapmap]
rs17671194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17671250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17672041	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17733008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053973	1.00[JPT][hapmap]
rs34088794	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3803358	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55788133	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs55982218	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56044352	1.00[AFR][1000 genomes]
rs56190115	1.00[AFR][1000 genomes]
rs56334337	1.00[AFR][1000 genomes]
rs679882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164132	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172000	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027487	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033303	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8033938	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037207	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8040755	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs7169404	C15orf23	cis	parietal	SCAN
rs7169404	SPTBN5	cis	cerebellum	SCAN
rs7169404	KNSTRN	cis	Esophagus Mucosa	GTEx
rs7169404	C15orf23	cis	cerebellum	SCAN
rs7169404	KNSTRN	cis	Artery Aorta	GTEx
rs7169404	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs7169404	LPCAT4	cis	parietal	SCAN
rs7169404	IVD	cis	Thyroid	GTEx
rs7169404	IVD	cis	Artery Tibial	GTEx
rs7169404	IVD	cis	Esophagus Muscularis	GTEx
rs7169404	IVD	cis	parietal	SCAN
rs7169404	C15orf23	Cis_1M	lymphoblastoid	RTeQTL
rs7169404	IVD	cis	Nerve Tibial	GTEx
rs7169404	KNSTRN	cis	Esophagus Muscularis	GTEx
rs7169404	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs7169404	KNSTRN	cis	Heart Left Ventricle	GTEx
rs7169404	KNSTRN	cis	Whole Blood	GTEx
rs7169404	IVD	cis	Esophagus Mucosa	GTEx
rs7169404	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs7169404	IVD	cis	lymphoblastoid	seeQTL
rs7169404	IVD	cis	cerebellum	SCAN
rs7169404	KNSTRN	cis	lung	GTEx
rs7169404	STOM	trans	parietal	SCAN
rs7169404	C15orf23	cis	multi-tissue	Pritchard
rs7169404	KNSTRN	cis	Nerve Tibial	GTEx
rs7169404	KNSTRN	cis	Muscle Skeletal	GTEx
rs7169404	KNSTRN	cis	Artery Tibial	GTEx
rs7169404	IVD	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40674600-40675600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:40674600-40675600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:40674600-40676200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr15:40674800-40675600	Active TSS	Primary T cells from cord blood	blood
5	chr15:40674800-40675600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:40674800-40675600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:40674800-40675600	Active TSS	Brain Substantia Nigra	brain
8	chr15:40674800-40675600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr15:40674800-40675600	Active TSS	Ovary	ovary
10	chr15:40674800-40675600	Active TSS	Rectal Smooth Muscle	rectum
11	chr15:40674800-40675800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:40674800-40675800	Active TSS	Fetal Intestine Large	intestine
13	chr15:40674800-40675800	Flanking Active TSS	Fetal Muscle Trunk	muscle
14	chr15:40674800-40676000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:40674800-40676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:40674800-40676000	Active TSS	Aorta	Aorta
17	chr15:40674800-40676000	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr15:40674800-40676200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:40674800-40676200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:40674800-40676200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:40674800-40676200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr15:40674800-40676200	Active TSS	Fetal Kidney	kidney
23	chr15:40674800-40676400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr15:40675000-40675600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:40675000-40675600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:40675000-40675600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:40675000-40675600	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr15:40675000-40675600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:40675000-40675600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr15:40675000-40675600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr15:40675000-40675600	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr15:40675000-40675600	Active TSS	Brain Angular Gyrus	brain
33	chr15:40675000-40675600	Active TSS	Brain Anterior Caudate	brain
34	chr15:40675000-40675600	Active TSS	Brain Cingulate Gyrus	brain
35	chr15:40675000-40675600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:40675000-40675600	Active TSS	Colon Smooth Muscle	Colon
37	chr15:40675000-40675600	Active TSS	Duodenum Mucosa	Duodenum
38	chr15:40675000-40675600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr15:40675000-40675600	Active TSS	Fetal Brain Female	brain
40	chr15:40675000-40675600	Active TSS	Fetal Heart	heart
41	chr15:40675000-40675600	Active TSS	Stomach Mucosa	stomach
42	chr15:40675000-40675600	Active TSS	Dnd41	blood
43	chr15:40675000-40675600	Active TSS	HUVEC	blood vessel
44	chr15:40675000-40675800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:40675000-40675800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:40675000-40675800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr15:40675000-40675800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:40675000-40675800	Active TSS	Esophagus	oesophagus
49	chr15:40675000-40675800	Active TSS	Fetal Intestine Small	intestine
50	chr15:40675000-40675800	Active TSS	Fetal Lung	lung

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