Variant report

Variant	rs7164132
Chromosome Location	chr15:40675155-40675156
allele	A/C
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	EGR1	chr15:40674889-40675312	H1-hESC	embryonic stem cell:	n/a	chr15:40675104-40675118
2	GTF2F1	chr15:40674994-40675275	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:40674845-40675923	Hela-S3	cervix:	n/a	n/a
4	SP4	chr15:40674775-40675310	H1-hESC	embryonic stem cell:	n/a	chr15:40675051-40675062
5	YY1	chr15:40674707-40675416	SK-N-SH_RA	brain:	n/a	chr15:40675032-40675044
6	KAP1	chr15:40674902-40675346	U2OS	brain:	n/a	n/a
7	MYC	chr15:40674533-40675267	H1-hESC	embryonic stem cell:	n/a	chr15:40674946-40674955
8	GABPA	chr15:40674704-40675741	K562	blood:	n/a	n/a
9	POLR2A	chr15:40675033-40675689	GM12878	blood:	n/a	n/a
10	TCF7L2	chr15:40674885-40675349	HCT-116	colon:	n/a	n/a
11	YY1	chr15:40674543-40675341	SK-N-SH_RA	brain:	n/a	chr15:40675032-40675044
12	HCFC1	chr15:40674786-40675548	K562	blood:	n/a	n/a
13	YY1	chr15:40674657-40675239	GM12878	blood:	n/a	chr15:40675032-40675044
14	TAF1	chr15:40675030-40675323	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr15:40674992-40675316	HepG2	liver:	n/a	n/a
16	MXI1	chr15:40674992-40675262	K562	blood:	n/a	n/a
17	POLR2A	chr15:40674973-40675695	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr15:40674839-40675729	NB4	blood:	n/a	n/a
19	SIX5	chr15:40674816-40675298	GM12878	blood:	n/a	n/a
20	MAX	chr15:40674866-40675934	NB4	blood:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708
21	CEBPB	chr15:40674781-40675253	Hela-S3	cervix:	n/a	chr15:40674943-40674954 chr15:40674943-40674956
22	MAX	chr15:40674822-40675775	K562	blood:	n/a	chr15:40675694-40675704 chr15:40674946-40674955 chr15:40675693-40675708
23	SIN3AK20	chr15:40674760-40675716	MCF-7	breast:	n/a	n/a
24	ZNF143	chr15:40674994-40675432	Hela-S3	cervix:	n/a	n/a
25	EGR1	chr15:40674680-40675513	HCT-116	colon:	n/a	chr15:40675104-40675118
26	MXI1	chr15:40674975-40675818	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:40674949-40675655	MCF-7	breast:	n/a	n/a
28	MYC	chr15:40674993-40675920	MCF10A-Er-Src	breast:	n/a	chr15:40675694-40675704 chr15:40675693-40675708
29	MAX	chr15:40674903-40675361	SK-N-SH	brain:	n/a	chr15:40674946-40674955
30	BACH1	chr15:40674915-40675294	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr15:40674640-40675575	A549	lung:	n/a	chr15:40675032-40675044
32	TAF1	chr15:40675051-40675324	GM12892	blood:	n/a	n/a
33	REST	chr15:40674860-40675310	K562	blood:	n/a	n/a
34	POLR2A	chr15:40674880-40675823	HL-60	blood:	n/a	n/a
35	POLR2A	chr15:40674991-40675560	GM19193	blood:	n/a	n/a
36	POLR2A	chr15:40674952-40676140	K562	blood:	n/a	n/a
37	POLR2A	chr15:40674859-40675737	ECC-1	luminal epithelium:	n/a	n/a
38	SMARCB1	chr15:40674830-40675723	Hela-S3	cervix:	n/a	n/a
39	SIN3AK20	chr15:40674903-40675465	SK-N-SH	brain:	n/a	n/a
40	RFX5	chr15:40674891-40675347	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr15:40674846-40675878	K562	blood:	n/a	n/a
42	CHD2	chr15:40674685-40675308	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZKSCAN1	chr15:40674872-40675306	Hela-S3	cervix:	n/a	n/a
44	CREB1	chr15:40674728-40675622	HepG2	liver:	n/a	n/a
45	POLR2A	chr15:40674968-40675431	GM12891	blood:	n/a	n/a
46	POLR2A	chr15:40674988-40675632	GM15510	blood:	n/a	n/a
47	YY1	chr15:40674674-40675346	H1-hESC	embryonic stem cell:	n/a	chr15:40675032-40675044
48	SRF	chr15:40674995-40675239	GM12878	blood:	n/a	n/a
49	TAF1	chr15:40674859-40675572	K562	blood:	n/a	n/a
50	JUN	chr15:40674684-40675284	H1-hESC	embryonic stem cell:	n/a	n/a

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
ENSG00000128944	Chromatin interaction
ENSG00000140323	Chromatin interaction
ENSG00000128928	Chromatin interaction
ENSG00000259714	Chromatin interaction
ENSG00000261374	Chromatin interaction
ENSG00000083123	Chromatin interaction
ENSG00000259368	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 29 )

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

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11557072	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858714	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905240	1.00[JPT][hapmap]
rs16970709	1.00[JPT][hapmap]
rs16970758	1.00[JPT][hapmap]
rs17671194	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17671250	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[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17672041	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.94[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053973	1.00[JPT][hapmap]
rs34088794	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3803358	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55788133	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs55982218	1.00[AFR][1000 genomes];0.92[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]
rs7164321	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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166991	0.92[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];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169262	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]
rs7169404	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]
rs7172000	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026523	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027487	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033303	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8033938	0.92[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037207	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8040755	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[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:29)

SNP	Gene	Cis/trans	Tissue	Source
rs7164132	IVD	cis	Artery Tibial	GTEx
rs7164132	IVD	cis	lymphoblastoid	seeQTL
rs7164132	C15orf23	cis	multi-tissue	Pritchard
rs7164132	KNSTRN	cis	Esophagus Mucosa	GTEx
rs7164132	IVD	cis	cerebellum	SCAN
rs7164132	C15orf23	Cis_1M	lymphoblastoid	RTeQTL
rs7164132	KNSTRN	cis	Nerve Tibial	GTEx
rs7164132	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs7164132	KNSTRN	cis	Esophagus Muscularis	GTEx
rs7164132	IVD	cis	Esophagus Mucosa	GTEx
rs7164132	IVD	cis	lung	GTEx
rs7164132	KNSTRN	cis	lung	GTEx
rs7164132	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs7164132	KNSTRN	cis	Whole Blood	GTEx
rs7164132	IVD	cis	Esophagus Muscularis	GTEx
rs7164132	C15orf23	cis	parietal	SCAN
rs7164132	IVD	cis	parietal	SCAN
rs7164132	LPCAT4	cis	parietal	SCAN
rs7164132	C15orf23	cis	cerebellum	SCAN
rs7164132	KNSTRN	cis	Artery Aorta	GTEx
rs7164132	SPTBN5	cis	cerebellum	SCAN
rs7164132	IVD	cis	Nerve Tibial	GTEx
rs7164132	STOM	trans	parietal	SCAN
rs7164132	IVD	cis	Thyroid	GTEx
rs7164132	MAPKBP1	cis	parietal	SCAN
rs7164132	KNSTRN	cis	Artery Tibial	GTEx
rs7164132	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs7164132	KNSTRN	cis	Heart Left Ventricle	GTEx
rs7164132	KNSTRN	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40674200-40675200	Enhancers	Lung	lung
2	chr15:40674600-40675200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:40674600-40675400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:40674600-40675400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr15:40674600-40675400	Active TSS	Stomach Smooth Muscle	stomach
6	chr15:40674600-40675600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:40674600-40675600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:40674600-40676200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr15:40674800-40675200	Enhancers	Gastric	stomach
10	chr15:40674800-40675200	Flanking Active TSS	Hela-S3	cervix
11	chr15:40674800-40675400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr15:40674800-40675400	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr15:40674800-40675400	Active TSS	Colonic Mucosa	Colon
14	chr15:40674800-40675400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr15:40674800-40675400	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr15:40674800-40675600	Active TSS	Primary T cells from cord blood	blood
17	chr15:40674800-40675600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:40674800-40675600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:40674800-40675600	Active TSS	Brain Substantia Nigra	brain
20	chr15:40674800-40675600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr15:40674800-40675600	Active TSS	Ovary	ovary
22	chr15:40674800-40675600	Active TSS	Rectal Smooth Muscle	rectum
23	chr15:40674800-40675800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:40674800-40675800	Active TSS	Fetal Intestine Large	intestine
25	chr15:40674800-40675800	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr15:40674800-40676000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:40674800-40676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:40674800-40676000	Active TSS	Aorta	Aorta
29	chr15:40674800-40676000	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr15:40674800-40676200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:40674800-40676200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:40674800-40676200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:40674800-40676200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:40674800-40676200	Active TSS	Fetal Kidney	kidney
35	chr15:40674800-40676400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr15:40675000-40675200	Active TSS	Primary B cells from cord blood	blood
37	chr15:40675000-40675200	Active TSS	Primary hematopoietic stem cells	blood
38	chr15:40675000-40675200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:40675000-40675200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:40675000-40675200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:40675000-40675200	Active TSS	Brain Germinal Matrix	brain
42	chr15:40675000-40675200	Active TSS	Fetal Brain Male	brain
43	chr15:40675000-40675400	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr15:40675000-40675400	Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr15:40675000-40675400	Active TSS	Primary B cells from peripheral blood	blood
46	chr15:40675000-40675400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr15:40675000-40675400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr15:40675000-40675400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:40675000-40675400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:40675000-40675400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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