Variant report

Variant	rs17135724
Chromosome Location	chr7:5785999-5786000
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	chr7:5784409..5786222-chr7:5819780..5821882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011275	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10257204	0.90[CHB][hapmap]
rs10261277	0.90[CHB][hapmap]
rs11760723	0.84[ASN][1000 genomes]
rs17135752	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135757	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008415	0.89[CHB][hapmap]
rs2042110	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28580503	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28592990	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779091	0.82[ASW][hapmap]
rs3779095	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs3801009	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap]
rs3801017	0.85[ASN][1000 genomes]
rs55678664	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56351202	0.82[AMR][1000 genomes]
rs56364996	0.85[ASN][1000 genomes]
rs56390377	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56391533	0.82[AMR][1000 genomes]
rs57948142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971918	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription 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 miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
8	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
10	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
12	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
13	nsv830891	chr7:5726301-5895460	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv1028601	chr7:5748982-5919098	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
16	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
17	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
18	nsv464293	chr7:5778796-5891221	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv464294	chr7:5778796-5891221	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv605987	chr7:5778796-5891221	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv2764038	chr7:5785999-5893967	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17135724	MIR650	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5753200-5794400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:5762000-5820400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:5762800-5786000	Weak transcription	Fetal Kidney	kidney
4	chr7:5762800-5790200	Weak transcription	Small Intestine	intestine
5	chr7:5765200-5790400	Weak transcription	Psoas Muscle	Psoas
6	chr7:5768800-5798200	Weak transcription	Colonic Mucosa	Colon
7	chr7:5769200-5790200	Weak transcription	Pancreas	Pancrea
8	chr7:5774200-5800600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:5776800-5786600	Strong transcription	Fetal Thymus	thymus
10	chr7:5779200-5788000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:5779400-5789400	Weak transcription	HMEC	breast
12	chr7:5781200-5788400	Weak transcription	NHLF	lung
13	chr7:5781200-5790200	Weak transcription	Esophagus	oesophagus
14	chr7:5781200-5790600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:5781200-5792400	Weak transcription	Gastric	stomach
16	chr7:5781400-5786000	Weak transcription	K562	blood
17	chr7:5781400-5789800	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:5781400-5790200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr7:5781400-5790400	Weak transcription	Right Ventricle	heart
20	chr7:5781400-5790600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:5781400-5799600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:5781400-5816800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:5781800-5790600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr7:5782400-5787800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:5782800-5786800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr7:5782800-5794400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr7:5783200-5786200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:5783200-5786800	Strong transcription	HepG2	liver
29	chr7:5783600-5786800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:5783600-5789600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr7:5783600-5789800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:5783600-5790200	Weak transcription	Ovary	ovary
33	chr7:5783600-5790200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:5783600-5798200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:5783800-5787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:5783800-5787600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:5783800-5789800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:5783800-5789800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:5783800-5789800	Weak transcription	Brain Substantia Nigra	brain
40	chr7:5783800-5790400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:5784000-5786000	Weak transcription	Hela-S3	cervix
42	chr7:5784000-5786600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr7:5784000-5786800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:5784000-5790000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr7:5784000-5819600	Weak transcription	Fetal Heart	heart
46	chr7:5784200-5787000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:5784200-5787400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:5784200-5788000	Strong transcription	Primary B cells from cord blood	blood
49	chr7:5784200-5788200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:5784200-5789800	Weak transcription	Rectal Smooth Muscle	rectum

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