Variant report

Variant	rs3735066
Chromosome Location	chr7:56146004-56146005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56131866..56134691-chr7:56145964..56148262,2	MCF-7	breast:
2	chr7:56139442..56142282-chr7:56145954..56148779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129103	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13221255	0.88[ASN][1000 genomes]
rs13222500	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs13232756	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs13236894	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13238424	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[EUR][1000 genomes]
rs13238521	0.83[AFR][1000 genomes]
rs13238899	0.84[CHD][hapmap]
rs13239795	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs13241227	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13243072	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs13243725	0.89[EUR][1000 genomes]
rs13340526	0.89[EUR][1000 genomes]
rs2242510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498258	0.84[EUR][1000 genomes]
rs34057777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34287940	0.95[EUR][1000 genomes]
rs34304703	0.84[EUR][1000 genomes]
rs34372667	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34667212	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34719521	0.89[EUR][1000 genomes]
rs34874704	0.89[EUR][1000 genomes]
rs35092795	0.93[EUR][1000 genomes]
rs35160834	0.89[EUR][1000 genomes]
rs35210477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35307785	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35551160	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35557048	0.88[ASN][1000 genomes]
rs35704704	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35829286	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35928425	0.90[ASN][1000 genomes]
rs3813504	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs4360246	0.89[EUR][1000 genomes]
rs56917729	0.89[EUR][1000 genomes]
rs71543773	0.87[EUR][1000 genomes]
rs71543784	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71543785	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71543788	0.90[ASN][1000 genomes]
rs71543793	0.83[EUR][1000 genomes]
rs73343714	0.89[EUR][1000 genomes]
rs73343719	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3735066	SUMF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
4	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
5	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
8	chr7:56138800-56146800	Weak transcription	Aorta	Aorta
9	chr7:56138800-56146800	Weak transcription	HSMMtube	muscle
10	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:56139000-56146800	Weak transcription	HSMM	muscle
13	chr7:56139000-56147000	Weak transcription	NH-A	brain
14	chr7:56139200-56146400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:56140400-56152000	Strong transcription	Dnd41	blood
16	chr7:56140800-56153000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:56142000-56151600	Strong transcription	Thymus	Thymus
18	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
19	chr7:56142200-56149600	Weak transcription	Fetal Kidney	kidney
20	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:56142400-56146200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:56142400-56146200	Weak transcription	HepG2	liver
23	chr7:56142400-56146600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:56142400-56156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:56142600-56146200	Weak transcription	Right Atrium	heart
26	chr7:56142600-56146800	Weak transcription	Left Ventricle	heart
27	chr7:56142600-56146800	Weak transcription	Stomach Mucosa	stomach
28	chr7:56142600-56159800	Strong transcription	Fetal Intestine Small	intestine
29	chr7:56142800-56146600	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:56143400-56150400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:56143800-56151000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:56143800-56153200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:56144000-56146800	Strong transcription	Fetal Stomach	stomach
34	chr7:56144000-56147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:56144000-56147000	Strong transcription	Fetal Brain Female	brain
36	chr7:56144000-56147800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:56144000-56148000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:56144000-56151200	Strong transcription	Primary T cells from cord blood	blood
39	chr7:56144200-56146200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:56144200-56146600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:56144200-56146800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:56144200-56147400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:56144200-56147800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr7:56144200-56147800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:56144200-56147800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:56144200-56147800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:56144200-56147800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr7:56144200-56147800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:56144200-56147800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:56144200-56147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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