Variant report

Variant	rs7704442
Chromosome Location	chr5:36951321-36951322
allele	C/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	TCF12	chr5:36950535-36951342	SK-N-SH	brain:	n/a	n/a
2	BRCA1	chr5:36951118-36951430	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr5:36950606-36951430	SK-N-SH	brain:	n/a	n/a
4	FOS	chr5:36951059-36951390	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr5:36950823-36951395	SK-N-SH	brain:	n/a	n/a
6	E2F4	chr5:36951015-36951381	MCF10A-Er-Src	breast:	n/a	chr5:36951196-36951208
7	PBX3	chr5:36950583-36951332	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr5:36950581-36951370	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr5:36950664-36951477	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36743855..36746677-chr5:36948839..36952257,4	MCF-7	breast:
2	chr5:36945026..36947869-chr5:36950785..36953502,2	K562	blood:

Variant related genes	Relation type
NIPBL	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13156908	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13162626	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13164726	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13165105	0.89[EUR][1000 genomes]
rs13176635	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181330	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13181860	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13186745	0.92[EUR][1000 genomes]
rs13187028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16903418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17312211	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs188383	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213513	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs289216	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293753	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293754	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293775	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298973	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34079524	0.92[EUR][1000 genomes]
rs34218486	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34272373	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34697946	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34807025	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34911537	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127161	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35167018	0.93[EUR][1000 genomes]
rs35357341	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35394109	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35809470	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36035695	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776594	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3899482	0.89[EUR][1000 genomes]
rs58123624	0.94[EUR][1000 genomes]
rs62654860	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6868809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6894622	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71617772	0.90[EUR][1000 genomes]
rs71617774	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093888	0.92[EUR][1000 genomes]
rs7700441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716192	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' 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	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS 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 target site	27 gene(s)	inside rSNPs	diseases
6	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv1033562	chr5:36927652-36994811	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1023362	chr5:36927652-37010749	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
10	nsv1017947	chr5:36927652-37017180	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1029936	chr5:36927652-37025871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv1029319	chr5:36928654-37017180	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
13	nsv1030883	chr5:36932448-37039857	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	esv1803659	chr5:36935129-37039857	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	nsv1034694	chr5:36946454-36991605	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1015172	chr5:36946454-36993280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1033778	chr5:36946454-36994811	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1033928	chr5:36947293-37039857	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
19	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active 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	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36919800-36953000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:36919800-36961600	Weak transcription	K562	blood
3	chr5:36920400-36951400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:36924800-36955200	Weak transcription	Dnd41	blood
5	chr5:36927600-36961600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:36933200-36962000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:36936000-36951600	Weak transcription	Primary B cells from cord blood	blood
8	chr5:36939600-36954200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:36939600-36955400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:36940200-36955600	Weak transcription	Fetal Thymus	thymus
11	chr5:36940600-36956000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:36940600-36985400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:36940800-36956600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:36944200-36957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:36944400-36955200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:36944800-36955400	Weak transcription	Placenta	Placenta
17	chr5:36945400-36951600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr5:36945600-36952000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:36945800-36953600	Weak transcription	Fetal Heart	heart
20	chr5:36946000-36957000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:36946200-36952000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:36946200-36965000	Weak transcription	Psoas Muscle	Psoas
23	chr5:36946400-36955400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:36946400-36978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:36946600-36955200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:36946600-36957000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:36946600-36970000	Weak transcription	Left Ventricle	heart
28	chr5:36946600-36976000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:36946800-36951800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:36947400-36951400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:36947600-36955000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:36948200-36951600	Enhancers	Colon Smooth Muscle	Colon
33	chr5:36948400-36955000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:36948400-36985800	Weak transcription	Colonic Mucosa	Colon
35	chr5:36948600-36962000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:36948600-36996600	Weak transcription	HSMMtube	muscle
37	chr5:36948800-36961800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:36949000-36951600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr5:36949200-36951400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr5:36949200-36952200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr5:36949400-36951400	Enhancers	Rectal Smooth Muscle	rectum
42	chr5:36949600-36952000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:36949600-36952200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:36950000-36951800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr5:36950200-36951400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:36950200-36951600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:36950200-36951600	Enhancers	Fetal Kidney	kidney
49	chr5:36950200-36952000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr5:36950400-36951400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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