Variant report

Variant	rs10734924
Chromosome Location	chr12:123018894-123018895
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122984970..122986643-chr12:123016494..123019420,2	MCF-7	breast:
2	chr12:123018583..123020922-chr12:123025836..123027739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033030	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10744211	0.88[JPT][hapmap]
rs10744275	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10744287	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10773088	1.00[JPT][hapmap]
rs10773103	0.88[JPT][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs10773152	0.88[JPT][hapmap];0.83[TSI][hapmap]
rs10773208	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs10773302	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10846664	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs10846688	0.88[JPT][hapmap]
rs10846699	0.88[JPT][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs10846746	0.88[JPT][hapmap]
rs10846921	1.00[JPT][hapmap]
rs10846978	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10847179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10847242	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10847415	0.81[CEU][hapmap]
rs10998	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11058226	1.00[JPT][hapmap]
rs11058402	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12369858	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs1392236	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1473553	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1803290	0.88[JPT][hapmap]
rs1973463	0.88[JPT][hapmap]
rs2062506	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2173628	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2341439	0.88[JPT][hapmap];0.83[TSI][hapmap]
rs2342082	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3803005	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817011	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs4319547	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758643	0.88[JPT][hapmap]
rs4758666	0.88[JPT][hapmap]
rs4997380	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs61954972	0.83[EUR][1000 genomes]
rs61954973	0.83[EUR][1000 genomes]
rs6416298	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6488958	0.88[JPT][hapmap];0.83[TSI][hapmap]
rs6489071	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489156	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6489157	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6489158	0.83[ASN][1000 genomes]
rs6489159	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7294559	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs7295105	0.85[ASN][1000 genomes]
rs7295397	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301515	0.89[TSI][hapmap]
rs7307233	0.84[CEU][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs7307735	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309390	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7314638	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7316149	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316734	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7397990	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7954006	0.89[ASW][hapmap];0.86[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7955203	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7959238	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7964138	0.81[ASW][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7966094	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7972728	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9705654	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9988963	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10734924	RNF34	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123012400-123022000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:123012400-123029400	Weak transcription	Ovary	ovary
3	chr12:123012400-123035000	Weak transcription	Lung	lung
4	chr12:123012400-123036600	Weak transcription	Esophagus	oesophagus
5	chr12:123012400-123066000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:123012400-123114000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:123012400-123117000	Weak transcription	Pancreas	Pancrea
8	chr12:123012400-123121200	Weak transcription	Aorta	Aorta
9	chr12:123012600-123019400	Weak transcription	Placenta	Placenta
10	chr12:123012600-123021400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:123012600-123024400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:123012600-123031600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:123012600-123032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:123012600-123036600	Weak transcription	Left Ventricle	heart
15	chr12:123012600-123042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:123012600-123066200	Weak transcription	Psoas Muscle	Psoas
17	chr12:123012600-123095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:123012800-123020200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:123012800-123021400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:123012800-123027600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:123012800-123032000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:123012800-123032000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:123012800-123036200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:123012800-123036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:123012800-123037200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:123012800-123037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:123012800-123042000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:123012800-123042000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:123012800-123065800	Weak transcription	Brain Substantia Nigra	brain
30	chr12:123012800-123097400	Weak transcription	Brain Angular Gyrus	brain
31	chr12:123012800-123109200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:123013000-123021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:123013000-123021400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:123013000-123021400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:123013000-123021400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:123013000-123029400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:123013000-123029400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:123013000-123030800	Weak transcription	Adipose Nuclei	Adipose
39	chr12:123013000-123030800	Weak transcription	Fetal Lung	lung
40	chr12:123013000-123031800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:123013000-123037000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:123013000-123076400	Weak transcription	Right Ventricle	heart
43	chr12:123013000-123109200	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:123013200-123019000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:123013200-123020000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:123013200-123020800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:123013200-123021200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:123013200-123034000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:123013200-123035200	Weak transcription	Liver	Liver
50	chr12:123013200-123036200	Weak transcription	Fetal Kidney	kidney

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