Variant report

Variant	rs55982218
Chromosome Location	chr15:40728810-40728811
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	chr15:40728757-40729102	K562	blood:	n/a	n/a
2	ELF1	chr15:40728532-40729111	GM12878	blood:	n/a	chr15:40728671-40728680
3	MAX	chr15:40728290-40729325	H1-hESC	embryonic stem cell:	n/a	chr15:40729240-40729250
4	POLR2A	chr15:40728064-40734370	K562	blood:	n/a	n/a
5	TAF1	chr15:40728739-40729048	K562	blood:	n/a	n/a
6	POLR2A	chr15:40728734-40729520	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAZ	chr15:40728411-40729942	K562	blood:	n/a	chr15:40729709-40729718
8	ELF1	chr15:40728520-40728907	K562	blood:	n/a	chr15:40728671-40728680
9	HCFC1	chr15:40728731-40728811	K562	blood:	n/a	n/a
10	TBL1XR1	chr15:40728565-40728900	K562	blood:	n/a	n/a
11	TBL1XR1	chr15:40728809-40729135	K562	blood:	n/a	n/a
12	SIN3A	chr15:40728333-40730280	H1-hESC	embryonic stem cell:	n/a	chr15:40728560-40728573 chr15:40728707-40728718 chr15:40728404-40728417
13	CHD2	chr15:40728680-40729077	K562	blood:	n/a	n/a
14	POLR2A	chr15:40728308-40729492	SK-N-MC	brain:	n/a	n/a
15	EP300	chr15:40728736-40729007	K562	blood:	n/a	n/a
16	MAX	chr15:40728285-40729441	K562	blood:	n/a	chr15:40729240-40729250
17	EGR1	chr15:40728610-40729183	K562	blood:	n/a	chr15:40729025-40729047 chr15:40728940-40728953 chr15:40728797-40728812
18	HEY1	chr15:40728723-40729496	K562	blood:	n/a	n/a
19	POLR2A	chr15:40728417-40729327	PBDE	blood:	n/a	n/a
20	POLR2A	chr15:40728371-40729412	K562	blood:	n/a	n/a
21	POLR2A	chr15:40728390-40729500	K562	blood:	n/a	n/a
22	JUND	chr15:40728554-40728927	K562	blood:	n/a	n/a
23	YY1	chr15:40728780-40728994	K562	blood:	n/a	n/a
24	POLR2A	chr15:40728687-40728940	K562	blood:	n/a	n/a
25	EGR1	chr15:40728619-40729090	K562	blood:	n/a	chr15:40729025-40729047 chr15:40728940-40728953 chr15:40728797-40728812
26	POLR2A	chr15:40728435-40729521	K562	blood:	n/a	n/a
27	UBTF	chr15:40728455-40729430	K562	blood:	n/a	n/a
28	CTBP2	chr15:40728398-40730550	H1-hESC	embryonic stem cell:	n/a	n/a
29	HMGN3	chr15:40728170-40729168	K562	blood:	n/a	n/a
30	ZBTB7A	chr15:40728791-40729055	K562	blood:	n/a	n/a
31	RCOR1	chr15:40728436-40729149	K562	blood:	n/a	n/a
32	HDAC2	chr15:40728774-40729083	K562	blood:	n/a	n/a
33	ZBTB7A	chr15:40728412-40729566	K562	blood:	n/a	chr15:40729494-40729502
34	TBP	chr15:40728807-40729396	K562	blood:	n/a	n/a
35	POLR2A	chr15:40728363-40729494	K562	blood:	n/a	n/a
36	CBX3	chr15:40728659-40729113	K562	blood:	n/a	n/a
37	MAX	chr15:40728267-40728927	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZBTB7A	chr15:40728445-40728828	ECC-1	luminal epithelium:	n/a	n/a
39	CHD2	chr15:40728736-40729023	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40727012..40730697-chr15:40730781..40733287,4	MCF-7	breast:
2	chr15:40727351..40729122-chr15:40759443..40761752,2	K562	blood:
3	chr15:40675969..40678151-chr15:40728400..40731089,2	K562	blood:
4	chr15:40659345..40661369-chr15:40727468..40729133,3	K562	blood:
5	chr15:40720491..40723802-chr15:40727203..40729063,3	MCF-7	breast:
6	chr15:40659345..40661369-chr15:40727468..40729027,2	K562	blood:
7	chr15:40718096..40719599-chr15:40728786..40730552,2	K562	blood:

Variant related genes	Relation type
BAHD1	TF binding region
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11557072	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671194	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17671250	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17672041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17733008	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34088794	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3803358	1.00[AFR][1000 genomes]
rs55788133	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs56044352	1.00[AFR][1000 genomes]
rs56190115	1.00[AFR][1000 genomes]
rs56334337	1.00[AFR][1000 genomes]
rs7164132	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164321	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166991	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169262	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169404	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172000	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026523	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8027487	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs8033938	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037207	0.82[EUR][1000 genomes]
rs8040755	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs55982218	IVD	cis	Esophagus Muscularis	GTEx
rs55982218	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs55982218	KNSTRN	cis	Whole Blood	GTEx
rs55982218	KNSTRN	cis	lung	GTEx
rs55982218	IVD	cis	lung	GTEx
rs55982218	KNSTRN	cis	Artery Tibial	GTEx
rs55982218	KNSTRN	cis	Artery Aorta	GTEx
rs55982218	IVD	cis	Thyroid	GTEx
rs55982218	KNSTRN	cis	Esophagus Muscularis	GTEx
rs55982218	KNSTRN	cis	Heart Left Ventricle	GTEx
rs55982218	KNSTRN	cis	Nerve Tibial	GTEx
rs55982218	KNSTRN	cis	Muscle Skeletal	GTEx
rs55982218	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs55982218	KNSTRN	cis	Esophagus Mucosa	GTEx
rs55982218	IVD	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40727400-40729000	Flanking Bivalent TSS/Enh	Thymus	Thymus
2	chr15:40727600-40729400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:40727600-40729400	Bivalent Enhancer	Fetal Heart	heart
4	chr15:40727600-40730200	Bivalent Enhancer	Fetal Brain Male	brain
5	chr15:40727800-40729000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr15:40727800-40729200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:40727800-40729200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
8	chr15:40727800-40729400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:40727800-40729400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr15:40727800-40729400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:40727800-40729400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr15:40727800-40729400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
13	chr15:40727800-40729400	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr15:40727800-40729800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:40727800-40729800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:40727800-40729800	Enhancers	Spleen	Spleen
17	chr15:40728000-40729000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:40728000-40729000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:40728000-40729000	Flanking Active TSS	Pancreas	Pancrea
20	chr15:40728000-40729000	Flanking Active TSS	Right Ventricle	heart
21	chr15:40728000-40729200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:40728000-40729200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr15:40728000-40729200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:40728000-40729400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
31	chr15:40728000-40729400	Flanking Bivalent TSS/Enh	NHEK	skin
32	chr15:40728000-40729600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr15:40728000-40729600	Enhancers	Lung	lung
34	chr15:40728000-40729800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr15:40728000-40729800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr15:40728000-40730200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr15:40728000-40730200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr15:40728200-40729000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:40728200-40729000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:40728200-40729000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:40728200-40729000	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr15:40728200-40729000	Bivalent Enhancer	HMEC	breast
43	chr15:40728200-40729200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr15:40728200-40729200	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr15:40728200-40729200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr15:40728200-40729400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr15:40728200-40729400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:40728200-40729600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr15:40728200-40729600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr15:40728200-40729600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin

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