Variant report

Variant	rs9845457
Chromosome Location	chr3:135914476-135914477
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	chr3:135914302-135916148	HCT-116	colon:	n/a	n/a
2	SPI1	chr3:135914474-135914808	GM12878	blood:	n/a	n/a
3	E2F1	chr3:135914160-135916102	Hela-S3	cervix:	n/a	chr3:135915168-135915177 chr3:135914365-135914375 chr3:135915140-135915149 chr3:135914922-135914931 chr3:135914917-135914927 chr3:135915286-135915295 chr3:135914923-135914933 chr3:135914546-135914556 chr3:135914865-135914875
4	SIN3AK20	chr3:135914384-135916044	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:135913953-135916146	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr3:135913991-135916313	ECC-1	luminal epithelium:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
7	MAX	chr3:135914155-135916243	SK-N-SH	brain:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
8	RCOR1	chr3:135913884-135916159	K562	blood:	n/a	n/a
9	POLR2A	chr3:135914119-135916127	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:135913253-135916718	Hela-S3	cervix:	n/a	n/a
11	MAX	chr3:135914051-135916271	A549	lung:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
12	MAX	chr3:135913217-135916536	Hela-S3	cervix:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
13	POLR2A	chr3:135913647-135916523	GM12878	blood:	n/a	n/a
14	JUND	chr3:135913874-135916532	K562	blood:	n/a	chr3:135914641-135914650
15	CEBPB	chr3:135913614-135916084	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:135914209-135916175	GM12891	blood:	n/a	n/a
17	YY1	chr3:135914119-135916115	ECC-1	luminal epithelium:	n/a	chr3:135914868-135914882 chr3:135915137-135915148 chr3:135914540-135914554 chr3:135914867-135914876 chr3:135914920-135914934 chr3:135914545-135914556 chr3:135914548-135914557 chr3:135914447-135914456 chr3:135914917-135914931 chr3:135914922-135914933 chr3:135915140-135915149 chr3:135914811-135914821 chr3:135914545-135914554 chr3:135915847-135915861 chr3:135914925-135914934 chr3:135914926-135914940 chr3:135914794-135914803 chr3:135914864-135914873 chr3:135914447-135914461 chr3:135914884-135914895 chr3:135914508-135914517 chr3:135914922-135914931
18	GATA1	chr3:135913718-135916708	PBDE	blood:	n/a	chr3:135916401-135916417 chr3:135916405-135916412 chr3:135916404-135916414 chr3:135916402-135916412 chr3:135916398-135916419 chr3:135916405-135916412 chr3:135916405-135916412
19	TAF1	chr3:135914437-135916097	GM12891	blood:	n/a	n/a
20	YY1	chr3:135914218-135915159	H1-hESC	embryonic stem cell:	n/a	chr3:135914868-135914882 chr3:135915137-135915148 chr3:135914540-135914554 chr3:135914867-135914876 chr3:135914920-135914934 chr3:135914545-135914556 chr3:135914548-135914557 chr3:135914447-135914456 chr3:135914917-135914931 chr3:135914922-135914933 chr3:135915140-135915149 chr3:135914811-135914821 chr3:135914545-135914554 chr3:135914925-135914934 chr3:135914926-135914940 chr3:135914794-135914803 chr3:135914864-135914873 chr3:135914447-135914461 chr3:135914884-135914895 chr3:135914508-135914517 chr3:135914922-135914931
21	POLR2A	chr3:135913666-135916815	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXP2	chr3:135914212-135915999	PFSK-1	brain:	n/a	n/a
23	PAX5	chr3:135914195-135915988	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:135913804-135916144	K562	blood:	n/a	n/a
25	POLR2A	chr3:135914195-135916194	H1-neurons	neurons:	n/a	n/a
26	HEY1	chr3:135914304-135916164	K562	blood:	n/a	chr3:135915734-135915749 chr3:135914923-135914938 chr3:135914951-135914966
27	POLR2A	chr3:135914136-135916190	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:135914170-135916072	A549	lung:	n/a	n/a
29	POLR2A	chr3:135914220-135916102	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr3:135914313-135916133	K562	blood:	n/a	n/a
31	RAD21	chr3:135913232-135915992	IMR90	lung:	n/a	chr3:135915979-135915991 chr3:135914585-135914595
32	POLR2A	chr3:135914469-135916081	HepG2	liver:	n/a	n/a
33	GABPA	chr3:135914434-135914876	K562	blood:	n/a	n/a
34	POLR2A	chr3:135914343-135916269	HEK293	kidney:	n/a	n/a
35	POLR2A	chr3:135913750-135916687	PANC-1	pancreas:	n/a	n/a
36	SMC3	chr3:135912532-135916143	Hela-S3	cervix:	n/a	chr3:135913724-135913732
37	SMARCB1	chr3:135913209-135916210	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:135914448-135916129	GM12891	blood:	n/a	n/a
39	HEY1	chr3:135914398-135914700	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:135913228-135916672	Hela-S3	cervix:	n/a	n/a
41	YY1	chr3:135913783-135916053	GM12892	blood:	n/a	chr3:135914868-135914882 chr3:135915137-135915148 chr3:135914540-135914554 chr3:135914867-135914876 chr3:135914920-135914934 chr3:135914545-135914556 chr3:135914548-135914557 chr3:135914447-135914456 chr3:135914917-135914931 chr3:135914922-135914933 chr3:135915140-135915149 chr3:135914811-135914821 chr3:135914545-135914554 chr3:135915847-135915861 chr3:135914925-135914934 chr3:135914926-135914940 chr3:135914794-135914803 chr3:135914864-135914873 chr3:135914447-135914461 chr3:135914884-135914895 chr3:135914508-135914517 chr3:135914922-135914931
42	ELK1	chr3:135914434-135914577	GM12878	blood:	n/a	n/a
43	CREB1	chr3:135914301-135916101	H1-hESC	embryonic stem cell:	n/a	n/a
44	REST	chr3:135914382-135916143	HepG2	liver:	n/a	chr3:135915026-135915036 chr3:135914869-135914882
45	TCF12	chr3:135914074-135916214	ECC-1	luminal epithelium:	n/a	chr3:135915900-135915907
46	ELF1	chr3:135914169-135916119	MCF-7	breast:	n/a	chr3:135914508-135914517 chr3:135914870-135914882 chr3:135914867-135914876 chr3:135914925-135914934 chr3:135914447-135914456 chr3:135914441-135914450 chr3:135914442-135914454 chr3:135914863-135914875 chr3:135914545-135914554 chr3:135914548-135914557 chr3:135914921-135914933
47	STAT1	chr3:135914277-135914671	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:135913937-135916297	GM12892	blood:	n/a	n/a
49	POLR2A	chr3:135913212-135916188	GM19193	blood:	n/a	n/a
50	E2F6	chr3:135914280-135916120	Hela-S3	cervix:	n/a	chr3:135915168-135915177 chr3:135914365-135914375 chr3:135915140-135915149 chr3:135915516-135915527 chr3:135914922-135914931 chr3:135914917-135914927 chr3:135915286-135915295 chr3:135914923-135914933 chr3:135914546-135914556 chr3:135914865-135914875

No.	Distal block	Cell Line	Cell type
1	chr3:135913308..135916970-chr3:135973705..135976198,3	K562	blood:
2	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
3	chr3:119215904..119218714-chr3:135913674..135916504,2	MCF-7	breast:
4	chr3:135913367..135916027-chr7:2562315..2565000,2	MCF-7	breast:
5	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
6	chr3:135820865..135823533-chr3:135914221..135916346,2	K562	blood:
7	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
8	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
9	chr3:134203423..134206037-chr3:135913664..135915183,2	MCF-7	breast:
10	chr3:135913726..135915628-chr3:135923532..135925229,2	MCF-7	breast:
11	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
12	chr11:67120530..67121080-chr3:135914391..135915327,2	Hela-S3	cervix:
13	chr3:135873199..135876113-chr3:135913654..135915671,2	K562	blood:
14	chr3:135914058..135916023-chr3:135977800..135980119,2	MCF-7	breast:
15	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:

Variant related genes	Relation type
MSL2	TF binding region
ENSG00000106003	Chromatin interaction
ENSG00000073711	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000244740	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000175482	Chromatin interaction
ENSG00000241438	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935177	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1145106	0.81[JPT][hapmap]
rs1153877	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1154988	1.00[JPT][hapmap]
rs1278493	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1279086	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1279425	0.86[JPT][hapmap]
rs1279831	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1279840	0.86[JPT][hapmap]
rs1711171	0.86[JPT][hapmap]
rs3755636	0.86[JPT][hapmap]
rs3957816	1.00[JPT][hapmap]
rs4678428	0.86[JPT][hapmap]
rs483465	0.86[JPT][hapmap]
rs518972	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs548288	0.86[JPT][hapmap]
rs553018	0.83[CHB][hapmap]
rs556788	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs571513	0.86[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs595532	0.83[CHB][hapmap]
rs606725	0.86[JPT][hapmap]
rs619605	0.81[JPT][hapmap]
rs645040	1.00[JPT][hapmap]
rs650326	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs654237	0.81[JPT][hapmap]
rs655836	0.81[JPT][hapmap]
rs661739	1.00[JPT][hapmap]
rs667920	0.86[JPT][hapmap]
rs684773	1.00[JPT][hapmap]
rs687339	1.00[JPT][hapmap]
rs695983	0.81[JPT][hapmap]
rs696081	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs696516	0.81[JPT][hapmap]
rs696520	0.86[JPT][hapmap]
rs698270	0.81[JPT][hapmap]
rs7349597	0.89[ASN][1000 genomes]
rs7372313	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs834304	0.83[CHB][hapmap]
rs895894	1.00[JPT][hapmap]
rs9810089	0.82[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs9811753	0.82[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap]
rs9840812	1.00[JPT][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3438899	chr3:135913487-135916235	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9845457	MSL2	cis	cerebellum	SCAN
rs9845457	PCCB	cis	cerebellum	SCAN
rs9845457	PCCB	cis	parietal	SCAN
rs9845457	PCCB	cis	lymphoblastoid	seeQTL
rs9845457	MSL2	cis	parietal	SCAN
rs9845457	NCK1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135907400-135914600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr3:135910000-135915600	Active TSS	GM12878-XiMat	blood
3	chr3:135910000-135916400	Active TSS	Thymus	Thymus
4	chr3:135910200-135916400	Active TSS	Aorta	Aorta
5	chr3:135910400-135916200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:135910600-135916000	Active TSS	HSMM	muscle
7	chr3:135910600-135916200	Active TSS	Colon Smooth Muscle	Colon
8	chr3:135910600-135916200	Active TSS	Ovary	ovary
9	chr3:135910600-135916200	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:135910600-135916400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:135910600-135916400	Active TSS	Colonic Mucosa	Colon
12	chr3:135910800-135915800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:135910800-135915800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:135910800-135915800	Active TSS	HMEC	breast
15	chr3:135910800-135916000	Active TSS	NHLF	lung
16	chr3:135910800-135916200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:135910800-135916200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr3:135910800-135916200	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr3:135910800-135916200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:135910800-135916200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:135910800-135916200	Active TSS	NHDF-Ad	bronchial
22	chr3:135910800-135916400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:135910800-135916400	Active TSS	Fetal Intestine Large	intestine
24	chr3:135910800-135916800	Active TSS	K562	blood
25	chr3:135911000-135916200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:135911000-135916200	Active TSS	Hela-S3	cervix
27	chr3:135911200-135916000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr3:135911200-135916200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:135911200-135916200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:135911200-135916400	Active TSS	Fetal Kidney	kidney
31	chr3:135911400-135915400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:135911400-135915600	Active TSS	Primary T cells fromperipheralblood	blood
33	chr3:135911400-135916000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:135911400-135916200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:135911400-135916200	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:135911400-135916200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:135911400-135916600	Active TSS	Psoas Muscle	Psoas
38	chr3:135911400-135916600	Active TSS	Right Ventricle	heart
39	chr3:135911600-135916000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:135911600-135916400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr3:135911600-135916400	Active TSS	HSMMtube	muscle
42	chr3:135911800-135915600	Active TSS	NH-A	brain
43	chr3:135911800-135915800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr3:135911800-135916000	Active TSS	NHEK	skin
45	chr3:135911800-135916200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:135911800-135916200	Active TSS	Brain Angular Gyrus	brain
47	chr3:135911800-135916400	Active TSS	A549	lung
48	chr3:135912000-135915000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:135912000-135915600	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:135912000-135915800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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