Variant report

Variant	rs7965407
Chromosome Location	chr12:122193566-122193567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122192772..122195093-chr12:122197272..122199194,2	MCF-7	breast:
2	chr12:122185135..122187179-chr12:122190114..122193871,4	K562	blood:
3	chr12:122154279..122156536-chr12:122192092..122194688,2	MCF-7	breast:
4	chr12:122191528..122194366-chr12:122203960..122205884,2	MCF-7	breast:
5	chr12:122185663..122191226-chr12:122191401..122193743,7	MCF-7	breast:
6	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
7	chr12:122185565..122190641-chr12:122191748..122195885,9	MCF-7	breast:
8	chr12:122191495..122194594-chr12:122209584..122212747,5	MCF-7	breast:
9	chr12:122193178..122194758-chr12:122236438..122238242,2	K562	blood:
10	chr12:122170094..122172075-chr12:122191951..122194592,2	MCF-7	breast:
11	chr12:122192032..122196057-chr12:122196899..122200786,5	MCF-7	breast:
12	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
13	chr12:122148796..122151884-chr12:122191170..122194399,4	MCF-7	breast:
14	chr12:122151601..122153571-chr12:122191520..122194326,2	MCF-7	breast:
15	chr12:122188030..122190854-chr12:122192525..122194477,3	K562	blood:
16	chr12:122190885..122194340-chr12:122235096..122240241,5	MCF-7	breast:
17	chr12:122190799..122194662-chr12:122203499..122206586,3	MCF-7	breast:
18	chr12:122182089..122184011-chr12:122191407..122193970,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272849	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1107243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs28656299	0.94[EUR][1000 genomes]
rs3970421	1.00[EUR][1000 genomes]
rs55775605	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56379201	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56959328	0.94[EUR][1000 genomes]
rs57318156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57611711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58274150	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58534280	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58986108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61230721	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6486775	0.83[EUR][1000 genomes]
rs7294817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7310523	0.83[EUR][1000 genomes]
rs7313408	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73411779	0.94[EUR][1000 genomes]
rs73411780	0.94[EUR][1000 genomes]
rs73411782	0.94[EUR][1000 genomes]
rs73411785	0.94[EUR][1000 genomes]
rs73411786	1.00[EUR][1000 genomes]
rs7957751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7962125	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7962350	0.84[LWK][hapmap];0.81[TSI][hapmap]
rs7968717	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7978536	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980551	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9737587	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9739927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7965407	RHOF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
3	chr12:122159400-122194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:122179800-122211000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
6	chr12:122184800-122208000	Weak transcription	Colonic Mucosa	Colon
7	chr12:122186200-122193600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:122186200-122194000	Strong transcription	Fetal Brain Female	brain
9	chr12:122186200-122197400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:122186600-122200400	Weak transcription	Right Atrium	heart
11	chr12:122186800-122197200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:122187000-122195200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:122187000-122199600	Strong transcription	Fetal Stomach	stomach
14	chr12:122187000-122207600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:122187000-122208200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:122187200-122203400	Weak transcription	Hela-S3	cervix
17	chr12:122187200-122205600	Weak transcription	Fetal Lung	lung
18	chr12:122187400-122194600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:122187400-122198000	Strong transcription	Fetal Intestine Small	intestine
20	chr12:122187400-122200200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:122187400-122203400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:122187400-122213800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:122187400-122213800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:122187600-122194600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122188200-122194600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:122188400-122194400	Weak transcription	NH-A	brain
27	chr12:122188400-122194400	Weak transcription	NHEK	skin
28	chr12:122188400-122194600	Weak transcription	HMEC	breast
29	chr12:122188400-122195800	Weak transcription	Primary T cells from cord blood	blood
30	chr12:122188400-122203400	Weak transcription	Osteobl	bone
31	chr12:122188400-122205600	Weak transcription	Aorta	Aorta
32	chr12:122188400-122207400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:122188600-122194000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:122188600-122199200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:122188800-122193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:122188800-122194400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:122188800-122194400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:122188800-122194600	Weak transcription	NHLF	lung
39	chr12:122188800-122197600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:122188800-122203400	Weak transcription	HSMM	muscle
41	chr12:122188800-122205600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:122188800-122205600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:122189200-122194200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:122189200-122194400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:122189200-122210800	Weak transcription	GM12878-XiMat	blood
46	chr12:122189200-122211000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:122189400-122202800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr12:122189400-122203400	Weak transcription	K562	blood
49	chr12:122189600-122194400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:122190000-122194400	Weak transcription	Primary T cells fromperipheralblood	blood

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