Variant report

Variant	rs9635726
Chromosome Location	chr17:38020141-38020142
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	POLR2A	chr17:38019552-38022062	GM12891	blood:	n/a	n/a
2	RELA	chr17:38019794-38020816	GM18951	blood:	n/a	n/a
3	MAX	chr17:38020069-38020779	HCT-116	colon:	n/a	chr17:38020427-38020437
4	TCF12	chr17:38020051-38020726	A549	lung:	n/a	chr17:38020462-38020469
5	POLR2A	chr17:38019648-38022019	GM18505	blood:	n/a	n/a
6	POLR2A	chr17:38019769-38021967	GM18951	blood:	n/a	n/a
7	BCLAF1	chr17:38019864-38022044	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:38020082-38020814	GM12891	blood:	n/a	n/a
9	FOXA1	chr17:38020078-38020473	HepG2	liver:	n/a	chr17:38020244-38020259
10	STAT5A	chr17:38020095-38020737	GM12878	blood:	n/a	n/a
11	RELA	chr17:38019691-38020937	GM12891	blood:	n/a	n/a
12	MAZ	chr17:38020018-38020867	GM12878	blood:	n/a	n/a
13	SIN3A	chr17:38020044-38020753	GM12878	blood:	n/a	n/a
14	MAX	chr17:38020004-38020778	HepG2	liver:	n/a	chr17:38020427-38020437
15	FOXA2	chr17:38020138-38020378	HepG2	liver:	n/a	n/a
16	PAX5	chr17:38020136-38020731	GM12878	blood:	n/a	n/a
17	FOXM1	chr17:38019838-38020923	GM12878	blood:	n/a	n/a
18	FOXA1	chr17:38020095-38020675	HepG2	liver:	n/a	chr17:38020244-38020259
19	TBP	chr17:38019706-38020858	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:38019694-38020188	GM12891	blood:	n/a	n/a
21	STAT5A	chr17:38019721-38020867	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:38019684-38021913	GM19099	blood:	n/a	n/a
23	RELA	chr17:38019928-38021965	GM18526	blood:	n/a	n/a
24	FOXA1	chr17:38020098-38020634	HepG2	liver:	n/a	chr17:38020244-38020259
25	FOXM1	chr17:38019949-38020874	GM12878	blood:	n/a	n/a
26	MAX	chr17:38020138-38020748	H1-hESC	embryonic stem cell:	n/a	chr17:38020427-38020437
27	POLR2A	chr17:38019860-38021965	GM19193	blood:	n/a	n/a
28	RELA	chr17:38020033-38020826	GM19193	blood:	n/a	n/a
29	RELA	chr17:38019751-38020790	GM10847	blood:	n/a	n/a
30	CHD1	chr17:38019547-38020942	GM12878	blood:	n/a	chr17:38020481-38020491
31	MAX	chr17:38019920-38020912	A549	lung:	n/a	chr17:38020427-38020437
32	POLR2A	chr17:38019501-38022100	GM12878	blood:	n/a	n/a
33	FOXA1	chr17:38020057-38020384	T-47D	breast:	n/a	chr17:38020244-38020259
34	RAD21	chr17:38020044-38020736	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:38019545-38021836	GM12878	blood:	n/a	n/a
36	SETDB1	chr17:38019746-38020658	U2OS	brain:	n/a	n/a
37	GATA1	chr17:38019829-38021176	PBDE	blood:	n/a	n/a
38	POLR2A	chr17:38020105-38020813	GM12878	blood:	n/a	n/a
39	NFIC	chr17:38019476-38022542	GM12878	blood:	n/a	n/a
40	WRNIP1	chr17:38019978-38020775	GM12878	blood:	n/a	n/a
41	POLR2A	chr17:38019554-38022098	GM12892	blood:	n/a	n/a
42	POLR2A	chr17:38019854-38021879	GM12892	blood:	n/a	n/a
43	RELA	chr17:38019979-38020815	GM12892	blood:	n/a	n/a
44	RELA	chr17:38019623-38020913	GM15510	blood:	n/a	n/a
45	PML	chr17:38019701-38022084	GM12878	blood:	n/a	n/a
46	MXI1	chr17:38019716-38021539	GM12878	blood:	n/a	n/a
47	POLR2A	chr17:38020071-38020680	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr17:38019991-38020792	GM12878	blood:	n/a	n/a
49	RELA	chr17:38019632-38020888	GM12878	blood:	n/a	n/a
50	MAX	chr17:38020005-38020765	A549	lung:	n/a	chr17:38020427-38020437

No.	Distal block	Cell Line	Cell type
1	chr17:38016155..38020243-chr17:38021178..38026655,8	K562	blood:
2	chr17:38016485..38022109-chr17:38022345..38027890,7	K562	blood:
3	chr17:37893210..37895843-chr17:38018530..38020744,2	MCF-7	breast:

Variant related genes	Relation type
ZPBP2	TF binding region
ENSG00000141738	Chromatin interaction
ENSG00000186075	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008723	0.86[CHB][hapmap]
rs10445308	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10852936	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs11078925	0.86[CHB][hapmap]
rs11078926	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11078927	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11557466	0.86[CHB][hapmap]
rs11557467	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11870965	0.86[CHB][hapmap]
rs12450323	0.82[AMR][1000 genomes]
rs12603332	0.95[CHB][hapmap]
rs12936231	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12946510	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2290400	0.86[CHB][hapmap]
rs2305479	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2305480	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3816470	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs4794820	0.85[CHB][hapmap]
rs4795400	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs4795405	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7213668	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7216389	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7219923	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs8069176	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs8076131	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs869402	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs870830	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs907091	0.82[CHD][hapmap]
rs9303277	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9303280	0.84[CHB][hapmap]
rs9303281	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs9909593	0.82[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9635726	SNORA21	cis	parietal	SCAN
rs9635726	MED24	cis	parietal	SCAN
rs9635726	SPACA3	cis	parietal	SCAN
rs9635726	DHRS11	cis	cerebellum	SCAN
rs9635726	GSDMB	cis	cerebellum	SCAN
rs9635726	SLFN12L	cis	parietal	SCAN
rs9635726	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs9635726	SLFN12	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38017000-38020200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr17:38017400-38021000	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr17:38017800-38020600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:38017800-38020800	Active TSS	Primary B cells from cord blood	blood
5	chr17:38017800-38021000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr17:38017800-38021400	Active TSS	Primary B cells from peripheral blood	blood
7	chr17:38017800-38021400	Active TSS	Primary T cells fromperipheralblood	blood
8	chr17:38017800-38021400	Active TSS	GM12878-XiMat	blood
9	chr17:38018000-38021000	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr17:38018000-38021000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:38018200-38021000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr17:38019200-38020800	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr17:38019200-38021000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:38019200-38021000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:38019400-38020800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:38019600-38021200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:38019600-38021200	Active TSS	Thymus	Thymus
18	chr17:38019800-38020200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr17:38019800-38020200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr17:38019800-38020200	Active TSS	Liver	Liver
21	chr17:38019800-38020200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
22	chr17:38019800-38020200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
23	chr17:38019800-38020400	Bivalent Enhancer	HepG2	liver
24	chr17:38019800-38020800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:38019800-38020800	Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr17:38019800-38020800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
27	chr17:38019800-38020800	Bivalent/Poised TSS	Small Intestine	intestine
28	chr17:38020000-38020200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr17:38020000-38020200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr17:38020000-38020200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:38020000-38020200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:38020000-38020200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:38020000-38020200	Bivalent Enhancer	Brain Anterior Caudate	brain
34	chr17:38020000-38020200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr17:38020000-38020200	Bivalent Enhancer	Placenta	Placenta
36	chr17:38020000-38020200	Bivalent/Poised TSS	Fetal Stomach	stomach
37	chr17:38020000-38020200	Bivalent/Poised TSS	Psoas Muscle	Psoas
38	chr17:38020000-38020200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr17:38020000-38020200	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr17:38020000-38020200	Bivalent Enhancer	Dnd41	blood
41	chr17:38020000-38020200	Bivalent/Poised TSS	NH-A	brain
42	chr17:38020000-38020400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr17:38020000-38020400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr17:38020000-38020400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
45	chr17:38020000-38020400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
46	chr17:38020000-38020400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr17:38020000-38020400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
48	chr17:38020000-38020400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
49	chr17:38020000-38020400	Active TSS	Right Atrium	heart
50	chr17:38020000-38020400	Flanking Bivalent TSS/Enh	A549	lung

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