Variant report

Variant	rs3797388
Chromosome Location	chr5:75904300-75904301
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	JUN	chr5:75904179-75905228	K562	blood:	n/a	chr5:75904897-75904906

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75901625..75904371-chr5:75985828..75988323,2	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10462543	1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap]
rs11948805	0.82[CHB][hapmap]
rs12513400	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12523647	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs1501788	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs17680732	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs17680756	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs17680811	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs17748322	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2270908	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736394	0.82[CHB][hapmap]
rs3756514	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs3797382	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3912001	1.00[CEU][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs4289539	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704329	1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap]
rs4704340	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55699952	0.86[ASN][1000 genomes]
rs56110610	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56338424	0.86[ASN][1000 genomes]
rs58087114	0.83[ASN][1000 genomes]
rs60881227	0.88[ASN][1000 genomes]
rs61014011	0.88[ASN][1000 genomes]
rs61233297	0.85[ASN][1000 genomes]
rs869733	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs873787	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs879017	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
2	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
3	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
4	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
8	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr5:75891000-75911800	Weak transcription	Thymus	Thymus
13	chr5:75891200-75909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:75891200-75911800	Strong transcription	Liver	Liver
15	chr5:75892000-75910400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:75895200-75912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:75896800-75913800	Weak transcription	Pancreas	Pancrea
18	chr5:75898000-75908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:75899200-75904400	Weak transcription	K562	blood
20	chr5:75899600-75907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:75900400-75905200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:75900800-75907400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:75901000-75906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:75901200-75904800	Weak transcription	A549	lung
25	chr5:75901200-75911200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:75901200-75917000	Weak transcription	HUVEC	blood vessel
27	chr5:75901400-75912400	Weak transcription	Fetal Intestine Large	intestine
28	chr5:75901600-75907600	Weak transcription	Fetal Intestine Small	intestine
29	chr5:75902200-75905200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:75902400-75904400	Strong transcription	Placenta	Placenta
31	chr5:75902400-75905000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:75902400-75905200	Genic enhancers	Primary B cells from cord blood	blood
33	chr5:75902600-75919200	Strong transcription	Primary T cells from cord blood	blood
34	chr5:75903000-75906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:75903000-75907200	Weak transcription	GM12878-XiMat	blood
36	chr5:75903400-75908800	Weak transcription	Gastric	stomach
37	chr5:75903600-75904600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:75903600-75905000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:75903600-75905000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:75903600-75905200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:75903600-75905200	Enhancers	Fetal Stomach	stomach
42	chr5:75903600-75914800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:75903600-75917800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:75903800-75904600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:75903800-75905200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr5:75903800-75905200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:75903800-75906200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:75903800-75906800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:75903800-75907200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:75903800-75907200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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