Variant report

Variant	rs6740224
Chromosome Location	chr2:153032790-153032791
allele	A/C
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	chr2:153031706-153033177	GM18526	blood:	n/a	n/a
2	USF2	chr2:153031799-153032817	H1-hESC	embryonic stem cell:	n/a	chr2:153032731-153032747 chr2:153032284-153032300
3	RAD21	chr2:153032361-153032792	SK-N-SH_RA	brain:	n/a	chr2:153032572-153032582
4	POLR2A	chr2:153030848-153033298	GM12891	blood:	n/a	n/a
5	GABPA	chr2:153032068-153032855	HL-60	blood:	n/a	chr2:153032575-153032584
6	RCOR1	chr2:153031842-153033140	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:153031667-153032794	PANC-1	pancreas:	n/a	n/a
8	FOXM1	chr2:153031547-153032819	GM12878	blood:	n/a	n/a
9	RXRA	chr2:153031949-153032796	GM12878	blood:	n/a	n/a
10	YY1	chr2:153031990-153032835	ECC-1	luminal epithelium:	n/a	chr2:153032563-153032572 chr2:153032569-153032580
11	TCF7L2	chr2:153031782-153032809	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr2:153031778-153033038	HepG2	liver:	n/a	n/a
13	HCFC1	chr2:153031494-153032984	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:153031478-153033112	GM12892	blood:	n/a	n/a
15	GABPA	chr2:153031783-153032885	K562	blood:	n/a	chr2:153032575-153032584
16	TAF1	chr2:153031764-153032922	ECC-1	luminal epithelium:	n/a	n/a
17	ELF1	chr2:153031700-153032814	K562	blood:	n/a	chr2:153032272-153032285 chr2:153032508-153032519 chr2:153032509-153032518
18	POLR2A	chr2:153031694-153032986	HepG2	liver:	n/a	n/a
19	JUND	chr2:153031676-153032809	K562	blood:	n/a	n/a
20	YY1	chr2:153031836-153032871	GM12892	blood:	n/a	chr2:153032563-153032572 chr2:153032569-153032580
21	POLR2A	chr2:153031509-153032975	GM12892	blood:	n/a	n/a
22	BRCA1	chr2:153031907-153032854	HepG2	liver:	n/a	n/a
23	SIN3AK20	chr2:153031660-153032850	HepG2	liver:	n/a	n/a
24	MXI1	chr2:153031210-153033283	GM12878	blood:	n/a	chr2:153032714-153032729
25	SP1	chr2:153031769-153032823	GM12878	blood:	n/a	chr2:153031996-153032005 chr2:153031994-153032006 chr2:153031995-153032004 chr2:153031989-153032001 chr2:153031994-153032006 chr2:153031995-153032009
26	POLR2A	chr2:153031578-153032799	HCT-116	colon:	n/a	n/a
27	NFIC	chr2:153031372-153033290	GM12878	blood:	n/a	n/a
28	CTBP2	chr2:153031804-153032925	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr2:153031474-153032900	A549	lung:	n/a	chr2:153032549-153032562 chr2:153032837-153032857 chr2:153032841-153032854 chr2:153032841-153032854
30	BCL3	chr2:153031574-153032823	A549	lung:	n/a	chr2:153032739-153032748 chr2:153032510-153032519 chr2:153032273-153032282 chr2:153032561-153032570 chr2:153032443-153032456 chr2:153032571-153032584
31	POLR2A	chr2:153031801-153032912	HL-60	blood:	n/a	n/a
32	TCF12	chr2:153031475-153033011	A549	lung:	n/a	chr2:153032284-153032291
33	RAD21	chr2:153031612-153032936	MCF-7	breast:	n/a	chr2:153032572-153032582
34	MYBL2	chr2:153031406-153033288	HepG2	liver:	n/a	n/a
35	RAD21	chr2:153032381-153032799	Hela-S3	cervix:	n/a	chr2:153032572-153032582
36	RAD21	chr2:153031577-153032979	IMR90	lung:	n/a	chr2:153032572-153032582
37	MYC	chr2:153031529-153032886	K562	blood:	n/a	chr2:153032569-153032579
38	POLR2A	chr2:153031654-153032893	Hela-S3	cervix:	n/a	n/a
39	MEF2A	chr2:153031992-153032821	GM12878	blood:	n/a	n/a
40	ELF1	chr2:153031719-153032862	SK-N-SH	brain:	n/a	chr2:153032272-153032285 chr2:153032508-153032519 chr2:153032509-153032518
41	CHD2	chr2:153031686-153033104	K562	blood:	n/a	n/a
42	RAD21	chr2:153031624-153033031	A549	lung:	n/a	chr2:153032572-153032582
43	POLR2A	chr2:153031643-153033287	U87	brain:	n/a	n/a
44	E2F6	chr2:153031838-153032925	A549	lung:	n/a	chr2:153032563-153032572 chr2:153032736-153032745 chr2:153032575-153032584
45	POLR2A	chr2:153031719-153032879	PANC-1	pancreas:	n/a	n/a
46	SIN3AK20	chr2:153031672-153032945	MCF-7	breast:	n/a	n/a
47	POLR2A	chr2:153031643-153033071	U87	brain:	n/a	n/a
48	POLR2A	chr2:153031649-153032870	HUVEC	blood vessel:	n/a	n/a
49	KAP1	chr2:153031529-153033273	HEK293	kidney:	n/a	chr2:153031701-153031709
50	TEAD4	chr2:153032208-153033208	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:153032743-153032793	HCF	heart:	n/a
2	chr2:153032743-153032793	PrEC	prostate:	n/a
3	chr2:153032743-153032793	AG09319	gingival:	n/a
4	chr2:153032743-153032793	HIPEpiC	eye:	n/a
5	chr2:153032743-153032793	SAEC	small airway:	n/a
6	chr2:153032743-153032793	AG04449	skin:	fetal
7	chr2:153032743-153032793	ECC-1	luminal epithelium:	n/a
8	chr2:153032743-153032793	A549	lung:	n/a
9	chr2:153032743-153032793	H1-hESC	embryonic stem cell:	embryo
10	chr2:153032743-153032793	HMEC	breast:	n/a
11	chr2:153032743-153032793	Caco-2	colon:	n/a
12	chr2:153032743-153032793	GM06990	blood:	n/a
13	chr2:153032743-153032793	HCM	heart:	n/a
14	chr2:153032743-153032793	Hepatocyte	liver:	n/a
15	chr2:153032743-153032793	PANC-1	pancreas:	n/a
16	chr2:153032743-153032793	AG09309	skin:	n/a
17	chr2:153032743-153032793	U87	brain:	n/a
18	chr2:153032743-153032793	SK-N-MC	brain:	n/a
19	chr2:153032743-153032793	HRE	kidney:	n/a
20	chr2:153032743-153032793	Jurkat	blood:	n/a
21	chr2:153032743-153032793	GM19239	blood:	n/a
22	chr2:153032743-153032793	GM12891	blood:	n/a
23	chr2:153032743-153032793	ovcar-3	ovarian:	n/a
24	chr2:153032743-153032793	HCT-116	colon:	n/a
25	chr2:153032743-153032793	MCF10A-Er-Src	breast:	n/a
26	chr2:153032743-153032793	Hela-S3	cervix:	n/a
27	chr2:153032743-153032793	SKMC	muscle:	n/a
28	chr2:153032743-153032793	HAEpiC	amniotic membrane:	n/a
29	chr2:153032743-153032793	HEEpiC	esophagus:	n/a
30	chr2:153032743-153032793	ProgFib	skin:	n/a
31	chr2:153032743-153032793	HEK293	kidney:	embryo
32	chr2:153032743-153032793	HRCEpiC	kidney:	n/a
33	chr2:153032743-153032793	IMR90	lung:	fetal
34	chr2:153032743-153032793	HL-60	blood:	n/a
35	chr2:153032743-153032793	AG04450	lung:	fetal
36	chr2:153032743-153032793	HCPEpiC	choroid plexus:	n/a
37	chr2:153032743-153032793	BJ	skin:	n/a
38	chr2:153032743-153032793	HUVEC	blood vessel:	n/a
39	chr2:153032743-153032793	RPTEC	kidney:	n/a
40	chr2:153032743-153032793	SK-N-SH_RA	brain:	n/a
41	chr2:153032743-153032793	AoSMC	blood vessel:	n/a
42	chr2:153032743-153032793	BE2_C	brain:	n/a
43	chr2:153032743-153032793	CMK	blood:	n/a
44	chr2:153032743-153032793	SK-N-SH	brain:	n/a
45	chr2:153032743-153032793	NT2-D1	testis:	n/a
46	chr2:153032743-153032793	T-47D	breast:	n/a
47	chr2:153032743-153032793	GM12892	blood:	n/a
48	chr2:153032743-153032793	LNCaP	prostate:	n/a
49	chr2:153032743-153032793	NHBE	bronchial:	n/a
50	chr2:153032743-153032793	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153023910..153026125-chr2:153032784..153034657,2	K562	blood:
2	chr2:152684763..152686807-chr2:153031833..153033553,2	MCF-7	breast:
3	chr2:153030659..153033731-chr2:153574261..153576507,5	MCF-7	breast:
4	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:
5	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:
6	chr2:152954463..152956019-chr2:153031201..153033706,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FMNL2-1	chr2:153032565-153033071	XLOC_001710
2	lnc-FMNL2-1	chr2:153032568-153033071	NONHSAT074978

Variant related genes	Relation type
STAM2	TF binding region
STAM2	CpG island
ENSG00000162980	Chromatin interaction
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction
ENSG00000225214	Chromatin interaction
ENSG00000182389	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10178907	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10184862	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10200655	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10803946	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs10930916	0.82[CHB][hapmap]
rs10930958	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11693948	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12612031	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12617139	0.86[CHB][hapmap]
rs12617696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17398329	0.86[CHB][hapmap]
rs2345639	0.86[CHB][hapmap]
rs3768650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4664079	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4664082	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664089	0.81[MEX][hapmap]
rs4664531	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs4664534	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664536	0.91[CHD][hapmap]
rs6650771	0.86[CHB][hapmap]
rs6738680	0.86[CHB][hapmap]
rs7369093	0.82[AMR][1000 genomes]
rs7603232	0.86[CHB][hapmap];0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6740224	STAM2	cis	parietal	SCAN
rs6740224	STAM2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153030200-153033200	Active TSS	Psoas Muscle	Psoas
2	chr2:153030200-153033200	Active TSS	GM12878-XiMat	blood
3	chr2:153030400-153033200	Active TSS	Right Atrium	heart
4	chr2:153030400-153033400	Active TSS	HSMMtube	muscle
5	chr2:153030400-153033400	Active TSS	NHDF-Ad	bronchial
6	chr2:153030600-153032800	Active TSS	NH-A	brain
7	chr2:153030600-153033200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:153030600-153033200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:153030600-153033200	Active TSS	Fetal Intestine Large	intestine
10	chr2:153030800-153033000	Active TSS	Stomach Mucosa	stomach
11	chr2:153030800-153033200	Active TSS	Aorta	Aorta
12	chr2:153030800-153033200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:153030800-153033400	Active TSS	NHLF	lung
14	chr2:153031000-153032800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:153031000-153032800	Active TSS	Fetal Kidney	kidney
16	chr2:153031000-153032800	Active TSS	Rectal Smooth Muscle	rectum
17	chr2:153031000-153032800	Active TSS	HSMM	muscle
18	chr2:153031000-153032800	Active TSS	NHEK	skin
19	chr2:153031000-153033000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:153031000-153033000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:153031000-153033000	Active TSS	Fetal Muscle Leg	muscle
22	chr2:153031000-153033000	Active TSS	A549	lung
23	chr2:153031000-153033200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr2:153031000-153033200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:153031000-153033200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:153031000-153033200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:153031000-153033200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:153031000-153033200	Active TSS	Right Ventricle	heart
29	chr2:153031000-153033400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:153031000-153033600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:153031200-153032800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:153031200-153032800	Active TSS	Brain Angular Gyrus	brain
33	chr2:153031200-153032800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:153031200-153032800	Active TSS	HMEC	breast
35	chr2:153031200-153033000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr2:153031200-153033000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:153031200-153033000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:153031200-153033000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:153031200-153033000	Active TSS	Duodenum Mucosa	Duodenum
40	chr2:153031200-153033000	Active TSS	Gastric	stomach
41	chr2:153031200-153033000	Active TSS	Lung	lung
42	chr2:153031200-153033000	Active TSS	Hela-S3	cervix
43	chr2:153031200-153033200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:153031200-153033200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr2:153031200-153033200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:153031200-153033200	Active TSS	Fetal Muscle Trunk	muscle
47	chr2:153031200-153033200	Active TSS	Placenta	Placenta
48	chr2:153031200-153033200	Active TSS	Left Ventricle	heart
49	chr2:153031200-153033200	Active TSS	Ovary	ovary
50	chr2:153031200-153033200	Active TSS	Pancreas	Pancrea

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