Variant report

Variant	rs5759602
Chromosome Location	chr22:23489362-23489363
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	POLR2A	chr22:23489241-23490463	MCF10A-Er-Src	breast:	n/a	n/a
2	HDAC2	chr22:23486603-23489476	K562	blood:	n/a	n/a
3	POLR2A	chr22:23489207-23489407	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT5A	chr22:23488704-23489441	K562	blood:	n/a	n/a
5	CEBPB	chr22:23489097-23490191	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:52238455..52240953-chr22:23487999..23490190,2	MCF-7	breast:
2	chr22:23488142..23489912-chr22:23520735..23522440,2	MCF-7	breast:
3	chr22:19159140..19161731-chr22:23487977..23489996,2	K562	blood:

Variant related genes	Relation type
RTDR1	TF binding region
RAB36	TF binding region
ENSG00000186716	Chromatin interaction
ENSG00000236794	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2301554	0.84[CEU][hapmap]
rs5751591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5759600	0.84[CEU][hapmap]
rs756632	1.00[JPT][hapmap]
rs9612246	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803110	chr22:22731758-23497674	Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
3	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
4	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
8	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
9	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
16	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
17	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
18	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
19	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
20	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
22	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
23	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
24	esv34158	chr22:23216762-23499513	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
25	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
26	nsv544616	chr22:23474827-23495231	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	esv1801510	chr22:23478611-23491000	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5759602	BCR///FLJ42953///LOC644165///LOC728468	N/A	lymphoblastoid	RTeQTL
rs5759602	BCR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23487800-23490200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:23487800-23499000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr22:23488000-23489600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr22:23488000-23489600	Weak transcription	Esophagus	oesophagus
5	chr22:23488000-23490200	Weak transcription	Gastric	stomach
6	chr22:23488000-23491000	Enhancers	HepG2	liver
7	chr22:23488000-23499400	Weak transcription	Right Ventricle	heart
8	chr22:23488200-23489800	Weak transcription	Stomach Mucosa	stomach
9	chr22:23488200-23490400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr22:23488200-23490600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:23488200-23491400	Enhancers	Pancreas	Pancrea
12	chr22:23488200-23491800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:23488200-23492800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr22:23488200-23492800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr22:23488200-23494600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr22:23488200-23505800	Weak transcription	HSMMtube	muscle
17	chr22:23488400-23489400	Weak transcription	Fetal Lung	lung
18	chr22:23488400-23489800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr22:23488400-23490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr22:23488400-23490000	Weak transcription	Fetal Thymus	thymus
21	chr22:23488400-23490000	Enhancers	NH-A	brain
22	chr22:23488400-23490200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:23488400-23490400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr22:23488400-23490400	Enhancers	Osteobl	bone
25	chr22:23488400-23490600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr22:23488400-23490600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:23488400-23490800	Enhancers	Placenta	Placenta
28	chr22:23488400-23491800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:23488400-23491800	Weak transcription	Fetal Intestine Small	intestine
30	chr22:23488400-23491800	Weak transcription	Ovary	ovary
31	chr22:23488400-23492000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr22:23488400-23492200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:23488400-23493200	Weak transcription	Colon Smooth Muscle	Colon
34	chr22:23488400-23493400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr22:23488400-23493400	Weak transcription	Fetal Brain Female	brain
36	chr22:23488400-23494800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr22:23488400-23495000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr22:23488400-23499000	Weak transcription	Colonic Mucosa	Colon
39	chr22:23488400-23499000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr22:23488400-23499200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr22:23488400-23505800	Weak transcription	Brain Substantia Nigra	brain
42	chr22:23488600-23489400	Weak transcription	Primary B cells from cord blood	blood
43	chr22:23488600-23489400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:23488600-23489400	Weak transcription	NHEK	skin
45	chr22:23488600-23490400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:23488600-23490800	Enhancers	Stomach Smooth Muscle	stomach
47	chr22:23488600-23491000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:23488600-23491200	Weak transcription	Right Atrium	heart
49	chr22:23488600-23491600	Strong transcription	Fetal Stomach	stomach
50	chr22:23488600-23492000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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