Variant report

Variant	rs11706359
Chromosome Location	chr3:155588148-155588149
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	CEBPB	chr3:155587628-155588695	Hela-S3	cervix:	n/a	chr3:155588493-155588504
2	SMC3	chr3:155587823-155588668	Hela-S3	cervix:	n/a	chr3:155588197-155588207 chr3:155588424-155588434
3	HCFC1	chr3:155587045-155589834	Hela-S3	cervix:	n/a	n/a
4	MAX	chr3:155587780-155588283	SK-N-SH	brain:	n/a	n/a
5	IRF1	chr3:155587863-155588648	K562	blood:	n/a	chr3:155588426-155588440 chr3:155588201-155588215 chr3:155588124-155588144
6	CTCF	chr3:155587416-155589160	A549	lung:	n/a	chr3:155588393-155588411 chr3:155588395-155588408 chr3:155588028-155588037
7	POLR2A	chr3:155587743-155588971	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F4	chr3:155587665-155588635	MCF10A-Er-Src	breast:	n/a	chr3:155588338-155588345 chr3:155588431-155588441 chr3:155588342-155588352 chr3:155588427-155588436 chr3:155588602-155588614
9	MYC	chr3:155588013-155588150	MCF-7	breast:	n/a	n/a
10	ELF1	chr3:155587913-155588665	K562	blood:	n/a	chr3:155588535-155588544
11	POLR2A	chr3:155587750-155589947	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr3:155587812-155589870	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr3:155587873-155588237	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:155587845-155589692	Gliobla	brain:	n/a	n/a
15	POLR2A	chr3:155587841-155589683	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:155587927-155588252	HUVEC	blood vessel:	n/a	n/a
17	RAD21	chr3:155587464-155588728	SK-N-SH	brain:	n/a	chr3:155588395-155588409
18	MAFK	chr3:155587835-155588547	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:155587817-155588720	U87	brain:	n/a	n/a
20	MYC	chr3:155587624-155589380	A549	lung:	n/a	chr3:155588950-155588960 chr3:155589002-155589012 chr3:155589086-155589096 chr3:155589231-155589241 chr3:155588428-155588438
21	E2F6	chr3:155587933-155589683	K562	blood:	n/a	chr3:155589197-155589204 chr3:155589180-155589191 chr3:155588338-155588345 chr3:155589195-155589206 chr3:155588431-155588441 chr3:155589197-155589204 chr3:155588342-155588352 chr3:155588427-155588436 chr3:155589181-155589193 chr3:155588602-155588614 chr3:155589196-155589208 chr3:155588952-155588961 chr3:155589196-155589205 chr3:155589197-155589204
22	RAD21	chr3:155588069-155588601	H1-hESC	embryonic stem cell:	n/a	chr3:155588395-155588409
23	POLR2A	chr3:155587930-155588172	HepG2	liver:	n/a	n/a
24	MAZ	chr3:155587870-155589434	HepG2	liver:	n/a	chr3:155588950-155588960 chr3:155589002-155589012 chr3:155589086-155589096 chr3:155589231-155589241 chr3:155588428-155588438
25	SETDB1	chr3:155587852-155588187	U2OS	brain:	n/a	n/a
26	POLR2A	chr3:155587784-155589046	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:155587839-155588757	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr3:155587582-155590231	MCF10A-Er-Src	breast:	n/a	n/a
29	HEY1	chr3:155587825-155588713	HepG2	liver:	n/a	chr3:155588437-155588452 chr3:155588467-155588482 chr3:155588342-155588357
30	HDAC2	chr3:155587872-155588567	HepG2	liver:	n/a	chr3:155587998-155588007
31	GTF2F1	chr3:155587957-155588673	K562	blood:	n/a	n/a
32	SIN3AK20	chr3:155587874-155588662	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:155587744-155589703	MCF-7	breast:	n/a	n/a
34	ELK1	chr3:155587926-155588628	K562	blood:	n/a	n/a
35	GATA2	chr3:155587761-155588458	SH-SY5Y	brain:	n/a	chr3:155587999-155588006 chr3:155587999-155588009
36	SMC3	chr3:155587925-155588581	K562	blood:	n/a	chr3:155588197-155588207 chr3:155588424-155588434
37	POLR2A	chr3:155587744-155589760	GM12892	blood:	n/a	n/a
38	TBP	chr3:155587705-155588758	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:155587630-155590235	Hela-S3	cervix:	n/a	n/a
40	TAF1	chr3:155587849-155588756	MCF-7	breast:	n/a	n/a
41	RCOR1	chr3:155587485-155589644	K562	blood:	n/a	n/a
42	MAX	chr3:155587816-155589768	A549	lung:	n/a	chr3:155588950-155588960 chr3:155589002-155589012 chr3:155589086-155589096 chr3:155589231-155589241 chr3:155588428-155588438
43	POLR2A	chr3:155587828-155589780	K562	blood:	n/a	n/a
44	PBX3	chr3:155587832-155588640	A549	lung:	n/a	n/a
45	JUND	chr3:155587619-155589832	K562	blood:	n/a	chr3:155588953-155588962
46	GABPA	chr3:155587917-155588340	K562	blood:	n/a	n/a
47	SMARCB1	chr3:155587851-155589700	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr3:155587941-155588696	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr3:155587686-155589773	HepG2	liver:	n/a	chr3:155588950-155588960 chr3:155589002-155589012 chr3:155589086-155589096 chr3:155589231-155589241 chr3:155588428-155588438
50	POLR2A	chr3:155587560-155589776	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:155588136-155588186	IMR90	lung:	fetal
2	chr3:155588124-155588174	GM12892	blood:	n/a
3	chr3:155588136-155588186	AG09319	gingival:	n/a
4	chr3:155588124-155588174	Jurkat	blood:	n/a
5	chr3:155588136-155588186	Caco-2	colon:	n/a
6	chr3:155588124-155588174	AG04450	lung:	fetal
7	chr3:155588124-155588174	AG10803	skin:	n/a
8	chr3:155588124-155588174	HEEpiC	esophagus:	n/a
9	chr3:155588136-155588186	PFSK-1	brain:	n/a
10	chr3:155588136-155588186	HNPCEpiC	eye:	n/a
11	chr3:155588124-155588174	H1-hESC	embryonic stem cell:	embryo
12	chr3:155588136-155588186	SK-N-SH	brain:	n/a
13	chr3:155588124-155588174	HEK293	kidney:	embryo
14	chr3:155588136-155588186	AoSMC	blood vessel:	n/a
15	chr3:155588136-155588186	HEK293	kidney:	embryo
16	chr3:155588136-155588186	HCF	heart:	n/a
17	chr3:155588124-155588174	HRCEpiC	kidney:	n/a
18	chr3:155588136-155588186	NT2-D1	testis:	n/a
19	chr3:155588124-155588174	BE2_C	brain:	n/a
20	chr3:155588124-155588174	LNCaP	prostate:	n/a
21	chr3:155588136-155588186	SKMC	muscle:	n/a
22	chr3:155588124-155588174	ovcar-3	ovarian:	n/a
23	chr3:155588136-155588186	ECC-1	luminal epithelium:	n/a
24	chr3:155588124-155588174	IMR90	lung:	fetal
25	chr3:155588124-155588174	SK-N-SH_RA	brain:	n/a
26	chr3:155588136-155588186	NHDF-neo	bronchial:	n/a
27	chr3:155588136-155588186	SK-N-MC	brain:	n/a
28	chr3:155588136-155588186	HRCEpiC	kidney:	n/a
29	chr3:155588124-155588174	RPTEC	kidney:	n/a
30	chr3:155588136-155588186	GM19239	blood:	n/a
31	chr3:155588124-155588174	HRE	kidney:	n/a
32	chr3:155588136-155588186	NH-A	brain:	n/a
33	chr3:155588136-155588186	GM06990	blood:	n/a
34	chr3:155588136-155588186	HMEC	breast:	n/a
35	chr3:155588124-155588174	AG09319	gingival:	n/a
36	chr3:155588136-155588186	MCF-7	breast:	n/a
37	chr3:155588136-155588186	HRE	kidney:	n/a
38	chr3:155588124-155588174	U87	brain:	n/a
39	chr3:155588124-155588174	Hepatocyte	liver:	n/a
40	chr3:155588124-155588174	AG09309	skin:	n/a
41	chr3:155588124-155588174	HepG2	liver:	n/a
42	chr3:155588124-155588174	HCM	heart:	n/a
43	chr3:155588136-155588186	AG04449	skin:	fetal
44	chr3:155588124-155588174	Hela-S3	cervix:	n/a
45	chr3:155588124-155588174	ProgFib	skin:	n/a
46	chr3:155588136-155588186	CMK	blood:	n/a
47	chr3:155588136-155588186	HCPEpiC	choroid plexus:	n/a
48	chr3:155588136-155588186	NB4	blood:	n/a
49	chr3:155588136-155588186	Hela-S3	cervix:	n/a
50	chr3:155588124-155588174	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:155520264..155525290-chr3:155586627..155590296,8	K562	blood:
2	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
3	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:
4	chr3:155568718..155574348-chr3:155586235..155593210,15	K562	blood:
5	chr14:24036599..24037349-chr3:155587998..155588957,2	HCT-116	colon:
6	chr19:571619..572299-chr3:155588026..155588830,2	Hela-S3	cervix:
7	chr10:27530732..27532552-chr3:155587161..155588906,2	MCF-7	breast:
8	chr3:155520823..155524412-chr3:155585049..155590112,5	MCF-7	breast:
9	chr3:155522036..155526613-chr3:155586597..155592084,8	K562	blood:
10	chr3:155570444..155573449-chr3:155586982..155591161,10	MCF-7	breast:
11	chr3:155522507..155525053-chr3:155587874..155590161,2	MCF-7	breast:
12	chr3:155477418..155480054-chr3:155586699..155588871,2	MCF-7	breast:
13	chr20:52490662..52493657-chr3:155587949..155590436,2	MCF-7	breast:
14	chr3:155461486..155463918-chr3:155586998..155589713,4	K562	blood:
15	chr3:155586547..155588282-chr3:156889087..156891969,2	MCF-7	breast:
16	chr3:155569630..155574596-chr3:155585012..155589734,13	MCF-7	breast:

Variant related genes	Relation type
GMPS	TF binding region
GMPS	CpG island
ENSG00000214919	Chromatin interaction
ENSG00000267751	Chromatin interaction
ENSG00000241307	Chromatin interaction
ENSG00000169359	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000107897	Chromatin interaction
ENSG00000174928	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000241721	Chromatin interaction
ENSG00000262412	Chromatin interaction
ENSG00000213983	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10804773	0.92[CEU][hapmap]
rs10936020	0.92[CEU][hapmap]
rs13061037	0.89[CHD][hapmap];0.83[MEX][hapmap]
rs3772116	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs6773642	0.89[TSI][hapmap]
rs6809229	0.88[CEU][hapmap]
rs7633168	0.92[CEU][hapmap]
rs7651038	0.92[CEU][hapmap]
rs7652005	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3325134	chr3:155587683-155590231	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11706359	SLC33A1	cis	parietal	SCAN
rs11706359	SLC33A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155587400-155588200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:155587400-155590000	Active TSS	Aorta	Aorta
3	chr3:155587400-155590600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:155587400-155590600	Active TSS	HepG2	liver
5	chr3:155587400-155591000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:155587600-155588200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr3:155587600-155588200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr3:155587600-155588200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:155587600-155588200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr3:155587600-155588200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr3:155587600-155588200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:155587600-155588200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:155587600-155588200	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr3:155587600-155588200	Flanking Active TSS	HMEC	breast
15	chr3:155587600-155588200	Flanking Active TSS	NHEK	skin
16	chr3:155587600-155588600	Active TSS	Fetal Brain Female	brain
17	chr3:155587600-155590000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:155587600-155590000	Active TSS	Placenta Amnion	Placenta Amnion
19	chr3:155587600-155590000	Active TSS	HSMM	muscle
20	chr3:155587600-155590200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:155587600-155590200	Active TSS	Left Ventricle	heart
22	chr3:155587600-155590200	Active TSS	Right Atrium	heart
23	chr3:155587600-155590200	Active TSS	Right Ventricle	heart
24	chr3:155587600-155590200	Active TSS	A549	lung
25	chr3:155587600-155590400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:155587600-155590400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:155587600-155590400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:155587600-155590400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:155587600-155590800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:155587600-155591000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:155587800-155588200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:155587800-155588200	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr3:155587800-155588200	Flanking Active TSS	Placenta	Placenta
34	chr3:155587800-155588400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:155587800-155589400	Active TSS	Colonic Mucosa	Colon
36	chr3:155587800-155589800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:155587800-155589800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:155587800-155589800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:155587800-155589800	Active TSS	Esophagus	oesophagus
40	chr3:155587800-155589800	Active TSS	Lung	lung
41	chr3:155587800-155590000	Active TSS	Colon Smooth Muscle	Colon
42	chr3:155587800-155590000	Active TSS	Fetal Kidney	kidney
43	chr3:155587800-155590000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:155587800-155590000	Active TSS	Gastric	stomach
45	chr3:155587800-155590000	Active TSS	Psoas Muscle	Psoas
46	chr3:155587800-155590000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr3:155587800-155590000	Active TSS	Small Intestine	intestine
48	chr3:155587800-155590200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:155587800-155590200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:155587800-155590200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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