Variant report

Variant	rs757660
Chromosome Location	chr22:30793137-30793138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr22:30792756-30793608	Hela-S3	cervix:	n/a	n/a
2	SIN3A	chr22:30792746-30793198	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr22:30792811-30793454	MCF-7	breast:	n/a	n/a
4	POLR2A	chr22:30792868-30793193	MCF-7	breast:	n/a	n/a
5	CTCF	chr22:30793060-30793210	HVMF	connective:	n/a	n/a
6	POLR2A	chr22:30792944-30793315	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr22:30792881-30793248	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr22:30792711-30793383	U87	brain:	n/a	n/a
9	MAZ	chr22:30792829-30793350	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr22:30792914-30793175	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr22:30792683-30793203	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr22:30792723-30793269	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr22:30792802-30793220	HepG2	liver:	n/a	n/a
14	POLR2A	chr22:30792790-30793342	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr22:30792747-30793945	A549	lung:	n/a	n/a
16	POLR2A	chr22:30792901-30793143	HepG2	liver:	n/a	n/a
17	GABPA	chr22:30792798-30793770	H1-hESC	embryonic stem cell:	n/a	chr22:30793302-30793311 chr22:30793261-30793270
18	POLR2A	chr22:30792711-30793725	U87	brain:	n/a	n/a
19	POLR2A	chr22:30792907-30793211	GM12878	blood:	n/a	n/a
20	MAFK	chr22:30793003-30793150	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr22:30791787-30796585	GM12878	blood:	n/a	n/a
22	POLR2A	chr22:30792934-30793172	IMR90	lung:	n/a	n/a
23	POLR2A	chr22:30792829-30793212	U87	brain:	n/a	n/a
24	POLR2A	chr22:30792749-30793851	HepG2	liver:	n/a	n/a
25	POLR2A	chr22:30792944-30793208	A549	lung:	n/a	n/a
26	POLR2A	chr22:30792838-30793224	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr22:30792678-30793542	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr22:30792749-30793286	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr22:30792846-30793337	ProgFib	skin:	n/a	n/a
30	POLR2A	chr22:30792617-30795297	GM12878	blood:	n/a	n/a
31	POLR2A	chr22:30792819-30795221	Hela-S3	cervix:	n/a	n/a
32	MAX	chr22:30792606-30793239	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr22:30792781-30793211	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr22:30793080-30793230	HCPEpiC	choroid plexus:	n/a	n/a
35	POLR2A	chr22:30792783-30793376	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr22:30792827-30793277	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr22:30792633-30793292	HCT-116	colon:	n/a	n/a
38	MAX	chr22:30792749-30793379	MCF-7	breast:	n/a	n/a
39	POLR2A	chr22:30792862-30793468	A549	lung:	n/a	n/a
40	MAX	chr22:30792739-30793239	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr22:30792744-30793223	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr22:30793078-30793139	MCF-7	breast:	n/a	n/a
43	POLR2A	chr22:30792589-30793292	PBDE	blood:	n/a	n/a
44	CTCF	chr22:30793040-30793190	SK-N-SH_RA	brain:	n/a	n/a
45	POLR2A	chr22:30792722-30793223	H1-hESC	embryonic stem cell:	n/a	n/a
46	SIN3AK20	chr22:30792852-30793396	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr22:30792898-30793283	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr22:30792905-30793170	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr22:30792533-30793593	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr22:30792782-30793845	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:30793123-30793173	HUVEC	blood vessel:	n/a
2	chr22:30793123-30793173	HEK293	kidney:	embryo
3	chr22:30793123-30793173	NB4	blood:	n/a
4	chr22:30793123-30793173	HCM	heart:	n/a
5	chr22:30793123-30793173	SK-N-SH	brain:	n/a
6	chr22:30793123-30793173	GM12878	blood:	n/a
7	chr22:30793123-30793173	SKMC	muscle:	n/a
8	chr22:30793123-30793173	SAEC	small airway:	n/a
9	chr22:30793123-30793173	HCF	heart:	n/a
10	chr22:30793123-30793173	HEEpiC	esophagus:	n/a
11	chr22:30793123-30793173	HNPCEpiC	eye:	n/a
12	chr22:30793123-30793173	Caco-2	colon:	n/a
13	chr22:30793123-30793173	MCF-7	breast:	n/a
14	chr22:30793123-30793173	AG04450	lung:	fetal
15	chr22:30793123-30793173	HAEpiC	amniotic membrane:	n/a
16	chr22:30793123-30793173	A549	lung:	n/a
17	chr22:30793123-30793173	Hepatocyte	liver:	n/a
18	chr22:30793123-30793173	PANC-1	pancreas:	n/a
19	chr22:30793123-30793173	MCF10A-Er-Src	breast:	n/a
20	chr22:30793123-30793173	BE2_C	brain:	n/a
21	chr22:30793123-30793173	NHBE	bronchial:	n/a
22	chr22:30793123-30793173	HCPEpiC	choroid plexus:	n/a
23	chr22:30793123-30793173	GM19239	blood:	n/a
24	chr22:30793123-30793173	ProgFib	skin:	n/a
25	chr22:30793123-30793173	SK-N-MC	brain:	n/a
26	chr22:30793123-30793173	HRE	kidney:	n/a
27	chr22:30793123-30793173	RPTEC	kidney:	n/a
28	chr22:30793123-30793173	PrEC	prostate:	n/a
29	chr22:30793123-30793173	HRPEpiC	eye:	n/a
30	chr22:30793123-30793173	T-47D	breast:	n/a
31	chr22:30793123-30793173	CMK	blood:	n/a
32	chr22:30793123-30793173	BJ	skin:	n/a
33	chr22:30793123-30793173	Jurkat	blood:	n/a
34	chr22:30793123-30793173	GM12891	blood:	n/a
35	chr22:30793123-30793173	HCT-116	colon:	n/a
36	chr22:30793123-30793173	ovcar-3	ovarian:	n/a
37	chr22:30793123-30793173	HepG2	liver:	n/a
38	chr22:30793123-30793173	AG04449	skin:	fetal
39	chr22:30793123-30793173	ECC-1	luminal epithelium:	n/a
40	chr22:30793123-30793173	AG09319	gingival:	n/a
41	chr22:30793123-30793173	IMR90	lung:	fetal
42	chr22:30793123-30793173	SK-N-SH_RA	brain:	n/a
43	chr22:30793123-30793173	NH-A	brain:	n/a
44	chr22:30793123-30793173	U87	brain:	n/a
45	chr22:30793123-30793173	K562	blood:	n/a
46	chr22:30793123-30793173	NHDF-neo	bronchial:	n/a
47	chr22:30793123-30793173	LNCaP	prostate:	n/a
48	chr22:30793123-30793173	NT2-D1	testis:	n/a
49	chr22:30793123-30793173	AG09309	skin:	n/a
50	chr22:30793123-30793173	Hela-S3	cervix:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
2	chr22:30793027..30795107-chr22:30817004..30819701,2	K562	blood:
3	chr22:30779604..30781335-chr22:30790630..30793179,2	MCF-7	breast:
4	chr17:56736502..56738510-chr22:30792727..30794981,2	MCF-7	breast:
5	chr22:30792578..30793211-chr6:111195646..111196460,2	HCT-116	colon:
6	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

No data

Variant related genes	Relation type
SEC14L2	TF binding region
SEC14L2	CpG island
ENSG00000222915	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000123505	Chromatin interaction
ENSG00000272689	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1061660	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1061664	0.89[MEX][hapmap]
rs12106618	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2018514	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072157	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072158	0.89[MEX][hapmap];0.80[MKK][hapmap]
rs2072159	0.84[MEX][hapmap];0.80[MKK][hapmap]
rs2074651	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074732	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[MEX][hapmap]
rs2240422	0.82[CHB][hapmap];0.84[MEX][hapmap]
rs2283868	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283869	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28523826	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820010	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749090	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753092	0.80[EUR][1000 genomes]
rs5753093	0.80[EUR][1000 genomes]
rs5753109	0.81[EUR][1000 genomes]
rs5753116	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753117	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997628	0.81[EUR][1000 genomes]
rs5997629	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997641	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7292744	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73390209	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs757870	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs8138401	0.82[EUR][1000 genomes]
rs887098	0.90[AMR][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs757660	LIF	cis	cerebellum	SCAN
rs757660	SGSM1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30789200-30793600	Weak transcription	K562	blood
2	chr22:30792400-30793400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:30792400-30793400	Enhancers	Fetal Brain Male	brain
4	chr22:30792400-30793600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr22:30792400-30793800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:30792400-30794200	Active TSS	HSMM	muscle
7	chr22:30792600-30793400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:30792600-30793400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr22:30792600-30793600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr22:30792600-30793600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr22:30792600-30793600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr22:30792600-30793600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr22:30792600-30793600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr22:30792600-30793600	Active TSS	Left Ventricle	heart
15	chr22:30792600-30793600	Active TSS	A549	lung
16	chr22:30792600-30793600	Active TSS	NHDF-Ad	bronchial
17	chr22:30792600-30793800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:30792600-30793800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr22:30792600-30793800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr22:30792600-30794000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr22:30792600-30794000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
22	chr22:30792600-30794000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:30792600-30794000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:30792600-30794000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr22:30792600-30794000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
26	chr22:30792600-30794000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr22:30792600-30794200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr22:30792600-30794400	Active TSS	Right Ventricle	heart
29	chr22:30792600-30794800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr22:30792600-30795400	Enhancers	Spleen	Spleen
31	chr22:30792800-30793200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:30792800-30793200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
33	chr22:30792800-30793400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr22:30792800-30793400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:30792800-30793400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr22:30792800-30793400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr22:30792800-30793400	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr22:30792800-30793400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr22:30792800-30793400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr22:30792800-30793400	Active TSS	Fetal Brain Female	brain
41	chr22:30792800-30793400	Flanking Active TSS	Placenta	Placenta
42	chr22:30792800-30793400	Active TSS	GM12878-XiMat	blood
43	chr22:30792800-30793600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
44	chr22:30792800-30793600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr22:30792800-30793600	Active TSS	Brain Substantia Nigra	brain
46	chr22:30792800-30793600	Active TSS	Esophagus	oesophagus
47	chr22:30792800-30793600	Active TSS	Fetal Intestine Small	intestine
48	chr22:30792800-30793600	Active TSS	Psoas Muscle	Psoas
49	chr22:30792800-30793600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr22:30792800-30793600	Active TSS	Rectal Smooth Muscle	rectum

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