Variant report

Variant	rs1224487
Chromosome Location	chr6:36986917-36986918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:36985940-36987551	Hela-S3	cervix:	n/a	n/a
2	SPI1	chr6:36986519-36986935	K562	blood:	n/a	chr6:36986816-36986829
3	CTCF	chr6:36985780-36987455	MCF-7	breast:	n/a	chr6:36986115-36986133
4	TEAD4	chr6:36985911-36987391	ECC-1	luminal epithelium:	n/a	n/a
5	ZNF263	chr6:36986006-36987195	HEK293-T-REx	kidney:	n/a	chr6:36986371-36986392 chr6:36986270-36986279 chr6:36986267-36986276
6	RAD21	chr6:36985653-36987106	HCT-116	colon:	n/a	chr6:36986113-36986132
7	SMC3	chr6:36985928-36986922	HepG2	liver:	n/a	n/a
8	CTCF	chr6:36986840-36986990	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr6:36986898-36987148	MCF10A-Er-Src	breast:	n/a	n/a
10	NFIC	chr6:36985983-36987395	ECC-1	luminal epithelium:	n/a	chr6:36987057-36987073 chr6:36987013-36987030
11	CTCF	chr6:36985678-36987167	HCT-116	colon:	n/a	chr6:36986115-36986133
12	CTCF	chr6:36986780-36986930	GM06990	blood:	n/a	n/a
13	TEAD4	chr6:36986814-36987382	ECC-1	luminal epithelium:	n/a	n/a
14	RAD21	chr6:36985701-36987052	HCT-116	colon:	n/a	chr6:36986113-36986132
15	CTCF	chr6:36986800-36986950	HMEC	breast:	n/a	n/a
16	MAX	chr6:36986771-36987531	MCF-7	breast:	n/a	n/a
17	RAD21	chr6:36984773-36987677	SK-N-SH	brain:	n/a	chr6:36986113-36986132 chr6:36985544-36985557 chr6:36985604-36985617
18	RAD21	chr6:36985909-36986919	MCF-7	breast:	n/a	chr6:36986113-36986132
19	NFIC	chr6:36986464-36987398	ECC-1	luminal epithelium:	n/a	chr6:36987057-36987073 chr6:36987013-36987030
20	MAX	chr6:36986861-36987349	ECC-1	luminal epithelium:	n/a	n/a
21	SMC3	chr6:36985181-36987422	SK-N-SH	brain:	n/a	n/a
22	FOSL1	chr6:36986888-36987324	K562	blood:	n/a	n/a
23	SPI1	chr6:36986374-36987077	HL-60	blood:	n/a	chr6:36986816-36986829
24	MYC	chr6:36985897-36987262	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr6:36985850-36987042	HepG2	liver:	n/a	chr6:36986115-36986133
26	CTCF	chr6:36986780-36986930	BE2_C	brain:	n/a	n/a
27	CEBPB	chr6:36986848-36987319	MCF-7	breast:	n/a	n/a
28	CTCF	chr6:36985556-36987592	HCT-116	colon:	n/a	chr6:36986115-36986133
29	SRF	chr6:36986436-36987436	ECC-1	luminal epithelium:	n/a	n/a
30	SMC3	chr6:36985849-36987304	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr6:36985870-36986973	MCF-7	breast:	n/a	chr6:36986115-36986133
32	PRDM1	chr6:36986588-36987191	Hela-S3	cervix:	n/a	chr6:36986888-36986901
33	RAD21	chr6:36985794-36987291	ECC-1	luminal epithelium:	n/a	chr6:36986113-36986132
34	CTCF	chr6:36985245-36987544	SK-N-SH	brain:	n/a	chr6:36986115-36986133
35	ESR1	chr6:36986863-36987339	ECC-1	luminal epithelium:	n/a	n/a
36	TCF12	chr6:36986463-36987358	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr6:36986860-36987010	HPAF	blood vessel:	n/a	n/a
38	CTCF	chr6:36986860-36987010	AG09319	gingival:	n/a	n/a

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36985829..36988521-chr6:36988646..36990558,2	K562	blood:
2	chr6:36985713..36987315-chr6:37177177..37178923,41	K562	blood:
3	chr6:36926516..36929397-chr6:36985217..36986948,2	K562	blood:
4	chr6:36985833..36987427-chr6:37139677..37140666,12	MCF-7	breast:
5	chr6:36985689..36987067-chr6:37174835..37176439,10	MCF-7	breast:
6	chr6:36831717..36834035-chr6:36985083..36987828,2	K562	blood:
7	chr6:36984736..36987348-chr6:37138212..37139729,2	K562	blood:
8	chr6:36984774..36987733-chr6:36993476..36997065,5	K562	blood:
9	chr6:36851998..36854194-chr6:36984664..36987550,2	K562	blood:
10	chr6:36947258..36950041-chr6:36986048..36987573,2	MCF-7	breast:
11	chr6:36986055..36987477-chr6:37177799..37178902,22	MCF-7	breast:
12	chr6:36985904..36987716-chr6:37141908..37143451,2	MCF-7	breast:
13	chr6:36985258..36986956-chr6:37321041..37322902,2	MCF-7	breast:
14	chr6:36986301..36987208-chr6:37139732..37140870,3	MCF-7	breast:
15	chr6:36985701..36987115-chr6:37175477..37176997,13	K562	blood:
16	chr6:36986126..36987117-chr6:37176530..37177578,3	MCF-7	breast:
17	chr6:36985644..36987482-chr6:37177455..37178899,11	MCF-7	breast:
18	chr6:36928588..36930558-chr6:36986253..36988587,2	K562	blood:
19	chr6:36986123..36987013-chr6:36995872..36996986,3	K562	blood:
20	chr6:36733415..36734583-chr6:36985207..36986995,7	MCF-7	breast:
21	chr6:36986109..36986997-chr6:37018972..37019835,3	MCF-7	breast:
22	chr6:36952434..36955977-chr6:36983476..36987276,5	MCF-7	breast:
23	chr6:36852005..36855458-chr6:36984429..36987560,3	K562	blood:
24	chr6:36985845..36988567-chr6:37138212..37140631,3	K562	blood:
25	chr6:36951647..36954567-chr6:36984468..36987638,6	K562	blood:
26	chr6:36980695..36984451-chr6:36985282..36988423,5	K562	blood:
27	chr6:36986111..36987939-chr6:37176127..37178450,2	MCF-7	breast:
28	chr6:36985158..36987310-chr6:37189028..37190861,2	K562	blood:
29	chr6:36985952..36987180-chr6:37139557..37141095,24	K562	blood:
30	chr6:36986227..36987023-chr6:37179191..37179864,2	MCF-7	breast:

No data

Variant related genes	Relation type
FGD2	TF binding region
ENSG00000198663	Chromatin interaction
ENSG00000137193	Chromatin interaction
ENSG00000146192	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000112130	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1224488	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1224491	0.90[ASN][1000 genomes]
rs1228575	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547571	0.89[CEU][hapmap]
rs1724094	0.90[ASN][1000 genomes]
rs1753300	0.82[EUR][1000 genomes]
rs1753301	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2025998	0.92[ASN][1000 genomes]
rs4317401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4711482	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6457974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6457980	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6939869	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7750403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7751821	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs831484	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs831487	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs831489	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs831491	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs831497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs831499	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs831500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs831502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs865550	0.83[EUR][1000 genomes]
rs913499	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9296207	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs9366927	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9380637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	28 gene(s)	inside rSNPs	diseases
4	nsv885816	chr6:36965099-36999682	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515488	chr6:36978745-36989587	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3436059	chr6:36986674-36990872	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1224487	FGD2	cis	Skin Sun Exposed Lower leg	GTEx
rs1224487	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36974200-36987000	Weak transcription	Right Atrium	heart
2	chr6:36975400-36988600	Weak transcription	Gastric	stomach
3	chr6:36975600-36988200	Weak transcription	Esophagus	oesophagus
4	chr6:36975600-36989600	Weak transcription	Thymus	Thymus
5	chr6:36983400-36995000	Weak transcription	Lung	lung
6	chr6:36984600-36987200	Enhancers	Fetal Thymus	thymus
7	chr6:36984800-36987000	Enhancers	Brain Hippocampus Middle	brain
8	chr6:36984800-36987200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:36984800-36987200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:36984800-36989000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:36985200-36987000	Enhancers	Fetal Muscle Leg	muscle
12	chr6:36985200-36987000	Enhancers	Placenta	Placenta
13	chr6:36985200-36987200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:36985200-36987400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:36985200-36987400	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:36985200-36988200	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr6:36985400-36987000	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:36985400-36987000	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr6:36985400-36987200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:36985400-36987200	Enhancers	Brain Angular Gyrus	brain
21	chr6:36985400-36987400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr6:36985400-36987400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:36985400-36987400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:36985400-36987400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:36985400-36987400	Enhancers	Fetal Muscle Trunk	muscle
26	chr6:36985400-36987600	Enhancers	Brain Germinal Matrix	brain
27	chr6:36985600-36987000	Enhancers	Fetal Intestine Large	intestine
28	chr6:36985600-36987000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:36985600-36987000	Genic enhancers	GM12878-XiMat	blood
30	chr6:36985600-36987200	Genic enhancers	Primary B cells from cord blood	blood
31	chr6:36985600-36987200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:36985600-36987200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:36985600-36987200	Enhancers	Brain Anterior Caudate	brain
34	chr6:36985600-36987200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:36985600-36987200	Enhancers	HepG2	liver
36	chr6:36985600-36987200	Enhancers	K562	blood
37	chr6:36985600-36987400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:36985600-36987400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr6:36985600-36987400	Enhancers	Primary hematopoietic stem cells	blood
40	chr6:36985600-36987400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:36985600-36987400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr6:36985600-36987400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:36985600-36987400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:36985600-36987400	Enhancers	Colon Smooth Muscle	Colon
45	chr6:36985600-36987400	Enhancers	Fetal Stomach	stomach
46	chr6:36985600-36987600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:36985600-36987600	Enhancers	HMEC	breast
48	chr6:36985600-36988800	Enhancers	Fetal Heart	heart
49	chr6:36985800-36987000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:36985800-36987000	Enhancers	Fetal Intestine Small	intestine

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