Variant report

Variant	rs11097211
Chromosome Location	chr4:89978456-89978457
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	USF2	chr4:89978181-89978576	H1-hESC	embryonic stem cell:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
2	USF1	chr4:89978136-89978511	SK-N-SH_RA	brain:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
3	MYC	chr4:89977945-89978610	K562	blood:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
4	POLR2A	chr4:89977891-89978679	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:89978065-89978657	K562	blood:	n/a	n/a
6	MAX	chr4:89977947-89978619	K562	blood:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
7	USF2	chr4:89978167-89978687	K562	blood:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
8	TBP	chr4:89977949-89978544	GM12878	blood:	n/a	n/a
9	MAX	chr4:89977876-89978665	ECC-1	luminal epithelium:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
10	TAF1	chr4:89978052-89978590	K562	blood:	n/a	n/a
11	POLR2A	chr4:89978002-89978600	K562	blood:	n/a	n/a
12	ATF3	chr4:89978212-89978500	K562	blood:	n/a	chr4:89978377-89978386
13	TBP	chr4:89977975-89978603	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr4:89978108-89978617	A549	lung:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
15	MYC	chr4:89977901-89978627	K562	blood:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
16	MAFK	chr4:89978197-89978538	Hela-S3	cervix:	n/a	n/a
17	MYC	chr4:89978048-89978527	K562	blood:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
18	POLR2A	chr4:89978195-89978465	A549	lung:	n/a	n/a
19	POLR2A	chr4:89977989-89978600	K562	blood:	n/a	n/a
20	USF1	chr4:89978238-89978456	GM12878	blood:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
21	TAF1	chr4:89977900-89978583	PFSK-1	brain:	n/a	n/a
22	MYC	chr4:89977877-89978601	A549	lung:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
23	GTF2B	chr4:89978155-89978584	K562	blood:	n/a	n/a
24	SIX5	chr4:89978154-89978477	K562	blood:	n/a	n/a
25	REST	chr4:89977922-89978546	A549	lung:	n/a	n/a
26	EP300	chr4:89977647-89978684	K562	blood:	n/a	chr4:89978623-89978637
27	POLR2A	chr4:89978199-89978497	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr4:89978220-89978494	Gliobla	brain:	n/a	n/a
29	SIX5	chr4:89978235-89978496	K562	blood:	n/a	n/a
30	POLR2A	chr4:89977872-89978652	PBDE	blood:	n/a	n/a
31	EBF1	chr4:89978119-89978506	GM12878	blood:	n/a	n/a
32	MAX	chr4:89977846-89978705	HCT-116	colon:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
33	SIX5	chr4:89978002-89978722	A549	lung:	n/a	n/a
34	ZNF384	chr4:89977979-89978653	K562	blood:	n/a	n/a
35	TAF1	chr4:89978160-89978476	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr4:89977960-89978631	K562	blood:	n/a	n/a
37	IRF1	chr4:89977954-89978629	K562	blood:	n/a	chr4:89978508-89978521
38	USF2	chr4:89978089-89978612	Hela-S3	cervix:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
39	POLR2A	chr4:89978085-89978613	GM12878	blood:	n/a	n/a
40	MAFF	chr4:89977965-89978639	K562	blood:	n/a	n/a
41	USF1	chr4:89977995-89978683	K562	blood:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
42	POLR2A	chr4:89978010-89978707	U87	brain:	n/a	n/a
43	KAP1	chr4:89977666-89978618	U2OS	brain:	n/a	n/a
44	USF1	chr4:89978213-89978554	HepG2	liver:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
45	USF1	chr4:89978103-89978639	H1-hESC	embryonic stem cell:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
46	YY1	chr4:89978002-89978560	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr4:89978002-89978637	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr4:89978074-89978576	MCF-7	breast:	n/a	chr4:89978377-89978386 chr4:89978375-89978388 chr4:89978377-89978386 chr4:89978471-89978482 chr4:89978375-89978388 chr4:89978372-89978391 chr4:89978377-89978386
49	YY1	chr4:89978147-89978602	ECC-1	luminal epithelium:	n/a	n/a
50	USF1	chr4:89978138-89978542	A549	lung:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388

No.	Distal block	Cell Line	Cell type
1	chr12:129308036..129308806-chr4:89978207..89978742,2	HCT-116	colon:
2	chr4:89743956..89746323-chr4:89976893..89978969,2	K562	blood:
3	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:

Variant related genes	Relation type
FAM13A	TF binding region
ENSG00000139370	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10000140	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs10024807	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027874	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10029662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030342	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11097209	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507819	0.83[AMR][1000 genomes]
rs13113298	0.86[CEU][hapmap]
rs13115669	0.82[AMR][1000 genomes]
rs13140085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150503	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1343921	0.87[LWK][hapmap]
rs1588730	0.87[CEU][hapmap]
rs17014898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17014901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17014988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056012	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28379646	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34378169	0.91[ASN][1000 genomes]
rs34693890	0.95[ASN][1000 genomes]
rs36048928	0.95[ASN][1000 genomes]
rs59385067	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61286299	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532102	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67317338	0.95[ASN][1000 genomes]
rs6823660	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6826407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827398	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853075	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857969	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660377	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668782	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7674344	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874147	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11097211	FAM13A	cis	cerebellum	SCAN
rs11097211	MMRN1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:89975600-89978800	Active TSS	Duodenum Mucosa	Duodenum
3	chr4:89975800-89978800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:89976000-89978800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:89976000-89978800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:89976000-89978800	Active TSS	Aorta	Aorta
7	chr4:89976000-89978800	Active TSS	Right Atrium	heart
8	chr4:89976200-89978600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:89976200-89978600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:89976200-89978800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:89976200-89978800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr4:89976200-89978800	Active TSS	Ovary	ovary
13	chr4:89976400-89978800	Active TSS	HMEC	breast
14	chr4:89976600-89978600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:89976600-89978600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:89976600-89978600	Active TSS	A549	lung
17	chr4:89976600-89978600	Active TSS	NHLF	lung
18	chr4:89976600-89978800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:89976600-89978800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr4:89976600-89978800	Flanking Active TSS	HUVEC	blood vessel
21	chr4:89976600-89979000	Active TSS	Stomach Smooth Muscle	stomach
22	chr4:89976600-89979000	Active TSS	K562	blood
23	chr4:89976800-89978600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:89976800-89978600	Active TSS	HSMMtube	muscle
25	chr4:89976800-89978800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:89976800-89978800	Active TSS	Fetal Kidney	kidney
27	chr4:89976800-89978800	Active TSS	Fetal Muscle Leg	muscle
28	chr4:89977000-89978600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:89977000-89978600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:89977000-89978600	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr4:89977000-89978600	Active TSS	Hela-S3	cervix
32	chr4:89977000-89978800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr4:89977000-89978800	Active TSS	Adipose Nuclei	Adipose
34	chr4:89977000-89978800	Active TSS	Brain Hippocampus Middle	brain
35	chr4:89977000-89978800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:89977000-89978800	Active TSS	Fetal Brain Male	brain
37	chr4:89977000-89978800	Active TSS	Fetal Intestine Small	intestine
38	chr4:89977000-89978800	Active TSS	Fetal Muscle Trunk	muscle
39	chr4:89977000-89978800	Active TSS	Fetal Stomach	stomach
40	chr4:89977000-89978800	Active TSS	Psoas Muscle	Psoas
41	chr4:89977000-89978800	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:89977000-89978800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr4:89977000-89978800	Active TSS	NHDF-Ad	bronchial
44	chr4:89977200-89978600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr4:89977200-89978600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:89977200-89978600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:89977200-89978600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr4:89977200-89978600	Active TSS	Fetal Lung	lung
49	chr4:89977200-89978600	Active TSS	Rectal Smooth Muscle	rectum
50	chr4:89977200-89978800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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