Variant report

Variant	rs7661349
Chromosome Location	chr4:106066982-106066983
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	CHD1	chr4:106066572-106070456	IMR90	lung:	n/a	chr4:106067048-106067058 chr4:106067469-106067479
2	POLR2A	chr4:106066572-106069408	GM12878	blood:	n/a	n/a
3	CEBPB	chr4:106066251-106067175	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:106066699-106068489	GM12878	blood:	n/a	n/a
5	SIN3A	chr4:106066695-106069254	H1-hESC	embryonic stem cell:	n/a	chr4:106067015-106067024 chr4:106067017-106067026
6	FOXM1	chr4:106066345-106067033	GM12878	blood:	n/a	n/a
7	MXI1	chr4:106066605-106068302	GM12878	blood:	n/a	chr4:106067017-106067026 chr4:106067015-106067024
8	POLR2A	chr4:106066621-106067012	GM12891	blood:	n/a	n/a
9	FOXA1	chr4:106066768-106067208	HepG2	liver:	n/a	chr4:106067027-106067039
10	POLR2A	chr4:106066660-106069216	GM19193	blood:	n/a	n/a
11	MXI1	chr4:106066891-106068214	HepG2	liver:	n/a	chr4:106067017-106067026 chr4:106067015-106067024
12	FOXA1	chr4:106066770-106067232	HepG2	liver:	n/a	chr4:106067027-106067039
13	MAZ	chr4:106066515-106068385	GM12878	blood:	n/a	chr4:106067016-106067025 chr4:106067015-106067026 chr4:106067921-106067929 chr4:106067016-106067025 chr4:106067016-106067025 chr4:106067015-106067025 chr4:106067016-106067026
14	FOXA1	chr4:106066738-106067196	HepG2	liver:	n/a	chr4:106067027-106067039
15	MTA3	chr4:106066370-106069459	GM12878	blood:	n/a	n/a
16	USF1	chr4:106066911-106067102	SK-N-SH_RA	brain:	n/a	chr4:106067015-106067026
17	CTCF	chr4:106066840-106066990	GM12865	blood:	n/a	n/a
18	HA-E2F1	chr4:106066907-106068342	MCF-7	breast:	n/a	chr4:106068153-106068164 chr4:106067959-106067969 chr4:106068156-106068165 chr4:106067558-106067570
19	BCLAF1	chr4:106066636-106067413	GM12878	blood:	n/a	chr4:106066653-106066662 chr4:106066652-106066661
20	ATF2	chr4:106066420-106067557	GM12878	blood:	n/a	n/a
21	MAX	chr4:106066827-106068259	GM12878	blood:	n/a	chr4:106067016-106067025 chr4:106067015-106067026 chr4:106067921-106067929 chr4:106067016-106067025 chr4:106067016-106067025 chr4:106067015-106067025 chr4:106067016-106067026
22	POLR2A	chr4:106066574-106068846	GM12891	blood:	n/a	n/a
23	USF1	chr4:106066910-106067108	HepG2	liver:	n/a	chr4:106067015-106067026
24	PML	chr4:106066139-106069518	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:106066154-106067028	HL-60	blood:	n/a	n/a
26	FOXA2	chr4:106066843-106067349	A549	lung:	n/a	chr4:106067027-106067039
27	POLR2A	chr4:106066639-106068328	GM19099	blood:	n/a	n/a
28	BHLHE40	chr4:106066854-106066987	K562	blood:	n/a	n/a
29	RELA	chr4:106066650-106069307	GM12891	blood:	n/a	n/a
30	FOXM1	chr4:106066644-106068631	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr4:106066872-106068345	MCF-7	breast:	n/a	n/a
32	TBL1XR1	chr4:106066474-106068328	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:106066663-106069295	GM18505	blood:	n/a	n/a
34	MYC	chr4:106066352-106068261	NB4	blood:	n/a	chr4:106067016-106067025 chr4:106067015-106067026 chr4:106067921-106067929 chr4:106067016-106067025 chr4:106067016-106067025 chr4:106067015-106067025 chr4:106067016-106067026
35	USF1	chr4:106066904-106067113	HepG2	liver:	n/a	chr4:106067015-106067026
36	USF2	chr4:106066910-106067385	GM12878	blood:	n/a	n/a
37	STAT5A	chr4:106066439-106068409	GM12878	blood:	n/a	chr4:106066652-106066661 chr4:106066653-106066662
38	POLR2A	chr4:106066741-106068377	GM15510	blood:	n/a	n/a
39	CHD1	chr4:106066661-106068961	GM12878	blood:	n/a	chr4:106067048-106067058 chr4:106067469-106067479
40	CTCF	chr4:106066940-106067090	HAc	cerebellar:	n/a	n/a
41	CTCF	chr4:106066860-106067130	GM12867	blood:	n/a	n/a
42	CTCF	chr4:106066891-106067020	GM12878	blood:	n/a	n/a
43	USF1	chr4:106066802-106067204	H1-hESC	embryonic stem cell:	n/a	chr4:106067015-106067026
44	MAX	chr4:106066743-106068296	HepG2	liver:	n/a	chr4:106067016-106067025 chr4:106067015-106067026 chr4:106067921-106067929 chr4:106067016-106067025 chr4:106067016-106067025 chr4:106067015-106067025 chr4:106067016-106067026
45	FOXA1	chr4:106066887-106067173	T-47D	breast:	n/a	chr4:106067027-106067039
46	POLR2A	chr4:106066687-106069263	GM12892	blood:	n/a	n/a
47	BHLHE40	chr4:106066521-106068316	GM12878	blood:	n/a	n/a
48	RUNX3	chr4:106066242-106067720	GM12878	blood:	n/a	n/a
49	MAX	chr4:106066818-106067755	A549	lung:	n/a	chr4:106067016-106067025 chr4:106067015-106067026 chr4:106067016-106067025 chr4:106067016-106067025 chr4:106067015-106067025 chr4:106067016-106067026
50	CREB1	chr4:106066298-106068427	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:106066539..106069010-chr4:106392150..106395317,5	MCF-7	breast:
2	chr4:106066586..106070319-chr4:106392729..106397085,7	MCF-7	breast:
3	chr4:106064811..106067302-chr4:106067349..106069355,2	K562	blood:
4	chr4:106066580..106068131-chr4:106393738..106396130,2	K562	blood:
5	chr4:105812145..105831361-chr4:106062414..106073665,101	MCF-7	breast:
6	chr4:106061142..106064736-chr4:106066504..106068895,4	K562	blood:
7	chr4:106026817..106029073-chr4:106065423..106067037,2	MCF-7	breast:
8	chr4:106064096..106067013-chr4:106110754..106112380,2	MCF-7	breast:
9	chr17:73518941..73521322-chr4:106066748..106068503,2	MCF-7	breast:
10	chr10:5539087..5542053-chr4:106066148..106068545,2	MCF-7	breast:
11	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:
12	chr4:106022079..106026589-chr4:106064672..106069140,4	MCF-7	breast:
13	chr4:105883010..105897017-chr4:106062943..106072055,55	MCF-7	breast:
14	chr18:10679396..10682032-chr4:106065086..106068050,2	MCF-7	breast:
15	chr4:105884036..105898505-chr4:106054854..106072562,138	MCF-7	breast:
16	chr17:60554571..60556757-chr4:106065577..106067920,2	MCF-7	breast:
17	chr4:106064646..106070521-chr4:106098298..106104512,9	MCF-7	breast:
18	chr4:106057698..106064116-chr4:106066476..106070338,7	K562	blood:
19	chr4:105823235..105830393-chr4:106065333..106069817,8	MCF-7	breast:
20	chr3:31572844..31575028-chr4:106066590..106069409,2	MCF-7	breast:

Variant related genes	Relation type
TET2	TF binding region
ENSG00000182173	Chromatin interaction
ENSG00000163527	Chromatin interaction
ENSG00000146872	Chromatin interaction
ENSG00000154864	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000251259	Chromatin interaction
ENSG00000178372	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000251906	Chromatin interaction
ENSG00000251473	Chromatin interaction
ENSG00000073350	Chromatin interaction
ENSG00000168769	Chromatin interaction
ENSG00000251586	Chromatin interaction
ENSG00000248373	Chromatin interaction
ENSG00000252136	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10007915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10461139	0.93[EUR][1000 genomes]
rs11721948	0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11726786	0.87[EUR][1000 genomes]
rs13109676	0.93[EUR][1000 genomes]
rs1541374	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2189234	0.88[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs2454206	0.89[GIH][hapmap];0.89[MEX][hapmap]
rs2647257	0.92[ASW][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs2726491	0.92[ASW][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs34104813	0.84[EUR][1000 genomes]
rs4698932	0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs4699165	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55838312	0.82[AMR][1000 genomes]
rs62331159	0.86[AMR][1000 genomes]
rs62332760	0.89[AMR][1000 genomes]
rs6533181	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6818637	0.92[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6855629	0.92[ASW][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes]
rs7679673	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7661349	GUCY2D	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106061800-106067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:106062200-106067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:106064800-106071800	Active TSS	GM12878-XiMat	blood
4	chr4:106065400-106067000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:106065800-106067000	Weak transcription	Small Intestine	intestine
6	chr4:106066000-106067600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:106066200-106067000	Active TSS	Placenta	Placenta
8	chr4:106066200-106067400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr4:106066200-106067400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:106066200-106070000	Active TSS	Monocytes-CD14+_RO01746	blood
11	chr4:106066200-106070200	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr4:106066200-106070600	Active TSS	Primary monocytes fromperipheralblood	blood
13	chr4:106066200-106070800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr4:106066400-106067000	Flanking Active TSS	A549	lung
15	chr4:106066400-106067400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:106066400-106069000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:106066400-106069200	Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr4:106066400-106069200	Active TSS	Brain Angular Gyrus	brain
19	chr4:106066600-106067000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr4:106066600-106067000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr4:106066600-106067000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr4:106066600-106067000	Active TSS	Fetal Muscle Trunk	muscle
23	chr4:106066600-106067200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:106066600-106067200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr4:106066600-106067200	Flanking Active TSS	Fetal Heart	heart
26	chr4:106066600-106067200	Flanking Active TSS	HepG2	liver
27	chr4:106066600-106067400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:106066600-106067400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr4:106066600-106067400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr4:106066600-106067600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:106066600-106067600	Bivalent/Poised TSS	Thymus	Thymus
32	chr4:106066600-106069200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr4:106066600-106069200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:106066600-106069400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr4:106066600-106069400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:106066600-106069400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:106066600-106069400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr4:106066600-106069400	Active TSS	Brain Anterior Caudate	brain
39	chr4:106066600-106069600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr4:106066600-106069600	Active TSS	Rectal Smooth Muscle	rectum
41	chr4:106066600-106070200	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr4:106066600-106070200	Active TSS	Right Atrium	heart
43	chr4:106066600-106070200	Active TSS	NHDF-Ad	bronchial
44	chr4:106066600-106070400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr4:106066600-106070800	Active TSS	Duodenum Mucosa	Duodenum
46	chr4:106066600-106070800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:106066800-106067000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
48	chr4:106066800-106067000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:106066800-106067000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:106066800-106067000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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