Variant report

Variant	rs772174
Chromosome Location	chr2:96991492-96991493
allele	A/G
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	chr2:96990449-96992083	GM18505	blood:	n/a	n/a
2	POLR2A	chr2:96990373-96992120	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:96990382-96992035	GM12878	blood:	n/a	n/a
4	MTA3	chr2:96990214-96992028	GM12878	blood:	n/a	n/a
5	ZBTB7A	chr2:96990715-96991556	ECC-1	luminal epithelium:	n/a	n/a
6	MXI1	chr2:96990269-96992115	SK-N-SH	brain:	n/a	chr2:96990546-96990555 chr2:96990546-96990555
7	POLR2A	chr2:96991431-96992000	GM12878	blood:	n/a	n/a
8	RUNX3	chr2:96990392-96991675	GM12878	blood:	n/a	n/a
9	RCOR1	chr2:96990623-96991950	GM12878	blood:	n/a	n/a
10	HEY1	chr2:96990705-96991511	HepG2	liver:	n/a	chr2:96991072-96991087 chr2:96991063-96991078
11	STAT1	chr2:96991005-96991545	GM12878	blood:	n/a	chr2:96991014-96991026 chr2:96991039-96991051
12	ELF1	chr2:96990733-96992064	GM12878	blood:	n/a	n/a
13	PML	chr2:96990338-96992006	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr2:96991275-96991509	K562	blood:	n/a	n/a
15	TBL1XR1	chr2:96991414-96991795	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:96990680-96991928	HepG2	liver:	n/a	n/a
17	MXI1	chr2:96991380-96991796	H1-hESC	embryonic stem cell:	n/a	n/a
18	ELK1	chr2:96991188-96991641	GM12878	blood:	n/a	n/a
19	MAX	chr2:96990351-96991951	HepG2	liver:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
20	POLR2A	chr2:96990501-96992014	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:96990582-96992027	GM19193	blood:	n/a	n/a
22	POLR2A	chr2:96990592-96991981	GM18951	blood:	n/a	n/a
23	MAX	chr2:96990274-96991681	HepG2	liver:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
24	POLR2A	chr2:96990746-96991508	HEK293	kidney:	n/a	n/a
25	MYC	chr2:96990355-96991492	K562	blood:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
26	STAT5A	chr2:96991081-96991552	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:96990368-96992169	GM12891	blood:	n/a	n/a
28	CHD2	chr2:96991227-96991859	GM12878	blood:	n/a	n/a
29	E2F6	chr2:96990410-96991658	H1-hESC	embryonic stem cell:	n/a	chr2:96991495-96991507
30	UBTF	chr2:96991304-96991534	K562	blood:	n/a	n/a
31	ZBTB7A	chr2:96990644-96991598	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr2:96990576-96991797	SK-N-MC	brain:	n/a	n/a
33	RCOR1	chr2:96991131-96991584	HepG2	liver:	n/a	n/a
34	MTA3	chr2:96991192-96991772	GM12878	blood:	n/a	n/a
35	MXI1	chr2:96990419-96992017	GM12878	blood:	n/a	chr2:96990546-96990555 chr2:96990546-96990555
36	ZNF143	chr2:96990495-96991622	GM12878	blood:	n/a	chr2:96991097-96991115 chr2:96990992-96991010
37	POLR2A	chr2:96990892-96991769	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:96990290-96992072	Raji	blood:	n/a	n/a
39	POLR2A	chr2:96990738-96991529	HCT-116	colon:	n/a	n/a
40	MYBL2	chr2:96990546-96991543	HepG2	liver:	n/a	n/a
41	MAX	chr2:96990317-96991692	K562	blood:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
42	MAX	chr2:96990604-96991513	SK-N-SH	brain:	n/a	n/a
43	MAZ	chr2:96990575-96991593	HepG2	liver:	n/a	n/a
44	SIN3A	chr2:96990543-96991868	H1-hESC	embryonic stem cell:	n/a	chr2:96990980-96990993 chr2:96990546-96990555
45	MAX	chr2:96990568-96991499	ECC-1	luminal epithelium:	n/a	n/a
46	MAZ	chr2:96990377-96991510	GM12878	blood:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
47	MAX	chr2:96990398-96991881	GM12878	blood:	n/a	chr2:96990545-96990555 chr2:96990545-96990554 chr2:96990544-96990555 chr2:96990544-96990555 chr2:96990545-96990554 chr2:96990545-96990554
48	POLR2A	chr2:96990657-96991534	H1-hESC	embryonic stem cell:	n/a	n/a
49	EBF1	chr2:96991469-96992011	GM12878	blood:	n/a	n/a
50	MAX	chr2:96990702-96991598	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96967785..96972096-chr2:96987875..96991841,5	K562	blood:
2	chr2:96874014..96875585-chr2:96990690..96992909,2	K562	blood:
3	chr2:96990031..96992678-chr2:97425792..97428161,2	K562	blood:
4	chr2:96971195..96973076-chr2:96991103..96992730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230747	TF binding region
ITPRIPL1	TF binding region
ENSG00000158158	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1081717	0.95[EUR][1000 genomes]
rs2579505	0.80[CEU][hapmap]
rs4907304	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs582014	0.84[CEU][hapmap]
rs596069	0.92[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs749458	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs772156	0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs772159	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs772160	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs772173	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs772177	1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs772174	NEDD4	trans	lymphoblastoid	seeQTL
rs772174	ITPRIPL1	cis	lung	GTEx
rs772174	KIAA1310	cis	cerebellum	SCAN
rs772174	LOC285033	cis	parietal	SCAN
rs772174	ITPRIPL1	cis	Esophagus Mucosa	GTEx
rs772174	ZNF514	cis	parietal	SCAN
rs772174	ADRA2B	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96990200-96991800	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr2:96990400-96992000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:96990400-96992000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr2:96990400-96992000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr2:96990400-96992200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:96990600-96991600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:96990600-96991600	Active TSS	Brain Substantia Nigra	brain
8	chr2:96990600-96991600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr2:96990600-96991800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr2:96990600-96991800	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr2:96990600-96991800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
12	chr2:96990600-96991800	Active TSS	Right Atrium	heart
13	chr2:96990600-96991800	Bivalent/Poised TSS	NH-A	brain
14	chr2:96990600-96992000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:96990600-96992000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr2:96990600-96992000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr2:96990600-96992000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr2:96990600-96992000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:96990600-96992000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
20	chr2:96990600-96992000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr2:96990600-96992000	Bivalent/Poised TSS	NHLF	lung
22	chr2:96990600-96992200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:96990600-96992400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr2:96990600-96992600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr2:96990800-96991600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr2:96990800-96991600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:96990800-96991600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:96990800-96991600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:96990800-96991600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr2:96990800-96991600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:96990800-96991600	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr2:96990800-96991600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr2:96990800-96991600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
34	chr2:96990800-96991600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr2:96990800-96991600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
36	chr2:96990800-96991600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:96990800-96991600	Active TSS	Thymus	Thymus
38	chr2:96990800-96991800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:96990800-96991800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:96990800-96991800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:96990800-96991800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:96990800-96991800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:96990800-96991800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
44	chr2:96990800-96991800	Active TSS	Brain Anterior Caudate	brain
45	chr2:96990800-96991800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
46	chr2:96990800-96991800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr2:96990800-96991800	Active TSS	Fetal Kidney	kidney
48	chr2:96990800-96991800	Flanking Active TSS	Pancreas	Pancrea
49	chr2:96990800-96991800	Bivalent/Poised TSS	Psoas Muscle	Psoas
50	chr2:96990800-96991800	Active TSS	GM12878-XiMat	blood

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