Variant report

Variant	rs2227316
Chromosome Location	chr17:38170007-38170008
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	USF1	chr17:38169915-38170377	A549	lung:	n/a	n/a
2	ZNF143	chr17:38169985-38170329	K562	blood:	n/a	chr17:38170006-38170024
3	CTCF	chr17:38170002-38170302	A549	lung:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
4	YY1	chr17:38169968-38170250	K562	blood:	n/a	chr17:38170166-38170188
5	RAD21	chr17:38169770-38170416	HCT-116	colon:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
6	ZNF263	chr17:38169970-38170338	HEK293-T-REx	kidney:	n/a	n/a
7	UBTF	chr17:38169978-38170258	K562	blood:	n/a	n/a
8	RAD21	chr17:38169968-38170355	HepG2	liver:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
9	CTCF	chr17:38169968-38170309	GM12878	blood:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
10	NR3C1	chr17:38169988-38170525	A549	lung:	n/a	n/a
11	ELK1	chr17:38169978-38170236	Hela-S3	cervix:	n/a	n/a
12	MAX	chr17:38169915-38170408	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr17:38169968-38170267	K562	blood:	n/a	n/a
14	RAD21	chr17:38169973-38170360	MCF-7	breast:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
15	CTCF	chr17:38169999-38170332	Lung_OC	lung:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
16	RUNX3	chr17:38169985-38170318	GM12878	blood:	n/a	n/a
17	RCOR1	chr17:38169993-38170340	Hela-S3	cervix:	n/a	n/a
18	MBD4	chr17:38169922-38170390	HepG2	liver:	n/a	n/a
19	MAFK	chr17:38169993-38170271	K562	blood:	n/a	n/a
20	GATA2	chr17:38169967-38170333	HUVEC	blood vessel:	n/a	n/a
21	RAD21	chr17:38169928-38170370	ECC-1	luminal epithelium:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
22	RAD21	chr17:38169854-38170386	HepG2	liver:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
23	EP300	chr17:38169992-38170345	K562	blood:	n/a	n/a
24	MYBL2	chr17:38169873-38170349	HepG2	liver:	n/a	n/a
25	RAD21	chr17:38169967-38170374	H1-hESC	embryonic stem cell:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
26	CTCF	chr17:38169992-38170317	NHEK	skin:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
27	RCOR1	chr17:38169864-38170387	IMR90	lung:	n/a	n/a
28	RAD21	chr17:38169740-38170436	SK-N-SH	brain:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
29	CTCF	chr17:38169735-38170396	A549	lung:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
30	RAD21	chr17:38169986-38170361	A549	lung:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
31	MAX	chr17:38169997-38170320	NB4	blood:	n/a	n/a
32	CTCF	chr17:38169870-38170308	T-47D	breast:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
33	CTCF	chr17:38169982-38170316	Spleen_OC	spleen:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
34	GATA3	chr17:38169930-38170311	T-47D	breast:	n/a	n/a
35	MYBL2	chr17:38169866-38170403	HepG2	liver:	n/a	n/a
36	SMC3	chr17:38169981-38170370	GM12878	blood:	n/a	chr17:38170153-38170167 chr17:38170153-38170161
37	RAD21	chr17:38169995-38170355	K562	blood:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
38	GATA3	chr17:38170007-38170387	MCF-7	breast:	n/a	n/a
39	ATF2	chr17:38169978-38170368	GM12878	blood:	n/a	n/a
40	BHLHE40	chr17:38170005-38170382	K562	blood:	n/a	n/a
41	RAD21	chr17:38169940-38170387	IMR90	lung:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
42	CTCF	chr17:38169942-38170317	A549	lung:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
43	GTF2F1	chr17:38170007-38170373	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr17:38169982-38170328	GM19238	blood:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170254-38170275 chr17:38170153-38170174 chr17:38170156-38170166
45	RAD21	chr17:38169976-38170375	GM12878	blood:	n/a	chr17:38170157-38170167 chr17:38170155-38170168 chr17:38170152-38170171 chr17:38170253-38170272
46	ARID3A	chr17:38170002-38170301	HepG2	liver:	n/a	n/a
47	ZNF143	chr17:38170007-38170323	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr17:38169970-38170266	T-47D	breast:	n/a	chr17:38170154-38170167 chr17:38170151-38170169 chr17:38170154-38170163 chr17:38170153-38170174 chr17:38170156-38170166
49	SIN3A	chr17:38170002-38170353	H1-hESC	embryonic stem cell:	n/a	chr17:38170085-38170099
50	ZEB1	chr17:38170002-38170301	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38169675..38170683-chr17:38324320..38325447,7	K562	blood:
2	chr17:38169634..38170581-chr17:38182673..38183938,4	MCF-7	breast:
3	chr17:38169401..38172627-chr17:38277979..38280708,3	K562	blood:
4	chr17:38168785..38171760-chr17:38343651..38347238,3	K562	blood:
5	chr17:38169698..38170555-chr17:38182945..38183495,2	MCF-7	breast:
6	chr17:38169698..38170628-chr17:38242600..38243276,2	MCF-7	breast:
7	chr17:38169753..38170672-chr17:38347301..38348138,3	K562	blood:
8	chr17:38168576..38170277-chr17:38268230..38270228,2	K562	blood:
9	chr17:38169654..38170220-chr17:38231592..38232145,2	MCF-7	breast:
10	chr17:38028899..38029611-chr17:38169830..38170569,2	MCF-7	breast:
11	chr17:38169705..38170739-chr17:38231468..38232451,5	K562	blood:

Variant related genes	Relation type
CSF3	TF binding region
ENSG00000238793	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000008838	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11078932	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11555254	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555255	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654473	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2227325	1.00[ASN][1000 genomes]
rs2827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36006659	1.00[EUR][1000 genomes]
rs3859188	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58212353	0.98[EUR][1000 genomes]
rs6503529	1.00[EUR][1000 genomes]
rs7217241	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217694	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222093	1.00[EUR][1000 genomes]
rs7222556	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7224260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068076	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8073732	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080546	0.98[EUR][1000 genomes]
rs9894543	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912981	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9913535	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9916279	0.93[AFR][1000 genomes];0.98[EUR][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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2227316	MED24	cis	Muscle Skeletal	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38154600-38170200	Weak transcription	Esophagus	oesophagus
3	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
4	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
6	chr17:38155400-38170200	Weak transcription	Placenta	Placenta
7	chr17:38155800-38171800	Weak transcription	Spleen	Spleen
8	chr17:38164600-38171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:38166800-38173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr17:38166800-38173800	Weak transcription	Primary T cells from cord blood	blood
11	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:38167600-38170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:38169000-38170200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:38169000-38171400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:38169200-38172400	Enhancers	NHEK	skin
20	chr17:38169400-38170400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr17:38169400-38171800	Enhancers	HMEC	breast
22	chr17:38169600-38170400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr17:38169600-38171600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:38169600-38172400	Enhancers	Stomach Mucosa	stomach
25	chr17:38169600-38172600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:38169600-38173200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr17:38169800-38170200	Enhancers	Primary B cells from peripheral blood	blood
29	chr17:38169800-38170200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr17:38169800-38170200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:38169800-38170200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr17:38169800-38170200	Enhancers	Brain Substantia Nigra	brain
33	chr17:38169800-38170200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr17:38169800-38170200	Enhancers	HepG2	liver
35	chr17:38169800-38170400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr17:38169800-38170400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr17:38169800-38170400	Enhancers	Dnd41	blood
38	chr17:38169800-38170600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr17:38169800-38171000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:38169800-38171000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr17:38169800-38171000	Enhancers	Right Ventricle	heart
42	chr17:38169800-38171600	Enhancers	K562	blood
43	chr17:38169800-38172200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr17:38169800-38172400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr17:38169800-38173000	Enhancers	Fetal Stomach	stomach
46	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
47	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:38170000-38170200	Enhancers	Primary B cells from cord blood	blood
49	chr17:38170000-38170200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:38170000-38170200	Enhancers	Cortex derived primary cultured neurospheres	brain

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