Variant report

Variant	rs6488958
Chromosome Location	chr12:122880704-122880705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122880690..122882401-chr12:123012980..123014769,2	K562	blood:
2	chr12:122879653..122881712-chr12:122883701..122886016,2	MCF-7	breast:
3	chr12:122878851..122886809-chr12:122904517..122908613,16	MCF-7	breast:
4	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
5	chr12:122880014..122886193-chr12:123009799..123012848,10	K562	blood:
6	chr12:122877588..122886723-chr12:122904086..122910536,22	K562	blood:

Variant related genes	Relation type
ENSG00000111011	Chromatin interaction
ENSG00000184445	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10161534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10734915	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10734918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10734924	0.88[JPT][hapmap];0.83[TSI][hapmap]
rs10744192	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744208	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10744209	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744210	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744211	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744217	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744220	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10744287	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10773075	0.90[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10773088	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773152	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10773167	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773172	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773176	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773178	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773208	0.85[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10846664	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846688	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846764	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846826	0.95[AMR][1000 genomes]
rs10846830	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10846835	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10846920	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846921	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846931	0.84[EUR][1000 genomes]
rs10846978	0.85[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10847179	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10847242	0.88[JPT][hapmap]
rs10998	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs11057786	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057797	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057882	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058034	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11058209	0.83[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11058233	0.84[EUR][1000 genomes]
rs11058251	0.86[EUR][1000 genomes]
rs11058282	0.80[EUR][1000 genomes]
rs11058402	0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs11616082	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11836188	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12369858	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs12372756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12423420	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425970	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12581249	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473553	0.85[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap]
rs1553179	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1803290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1818050	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2173582	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2341439	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28730465	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34129612	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817011	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4039670	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4319547	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4758643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758644	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758645	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758646	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758662	0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4997380	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55834409	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488933	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488939	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488951	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6489002	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135419	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294559	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs7314638	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7316114	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7397299	0.85[EUR][1000 genomes]
rs7398014	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7952868	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7953007	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7956480	0.91[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7964138	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973869	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7974262	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7975747	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9788145	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9988963	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6488958	GTF2H3	cis	cerebellum	SCAN
rs6488958	NME2P1	cis	cerebellum	SCAN
rs6488958	B3GNT4	cis	cerebellum	SCAN
rs6488958	GATC	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122846000-122883800	Weak transcription	Aorta	Aorta
2	chr12:122856400-122884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:122862400-122883800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:122862600-122881600	Weak transcription	Thymus	Thymus
6	chr12:122862600-122883800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:122862800-122895600	Weak transcription	Small Intestine	intestine
8	chr12:122863000-122883600	Weak transcription	K562	blood
9	chr12:122863000-122883800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:122863200-122883800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:122863400-122883800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:122863400-122884000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:122863400-122884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:122863400-122884600	Weak transcription	Ovary	ovary
15	chr12:122863400-122897400	Weak transcription	Fetal Brain Female	brain
16	chr12:122863400-122897800	Weak transcription	Brain Substantia Nigra	brain
17	chr12:122863800-122883800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:122863800-122905000	Weak transcription	Dnd41	blood
19	chr12:122864000-122883800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:122864200-122884000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:122864400-122883800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:122865200-122880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:122865200-122883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:122865200-122885000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:122865400-122883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:122866400-122883600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:122866600-122883800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:122866600-122883800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:122866600-122883800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:122866600-122884000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:122866600-122884000	Weak transcription	Spleen	Spleen
32	chr12:122866600-122888400	Weak transcription	Gastric	stomach
33	chr12:122866800-122881200	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:122867000-122884000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:122867000-122885000	Weak transcription	Esophagus	oesophagus
36	chr12:122867200-122881200	Weak transcription	Lung	lung
37	chr12:122867200-122883800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:122868200-122883600	Weak transcription	HSMM	muscle
39	chr12:122870000-122884200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:122870200-122883800	Weak transcription	GM12878-XiMat	blood
41	chr12:122870400-122883800	Weak transcription	HSMMtube	muscle
42	chr12:122870400-122884000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:122870800-122881200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:122870800-122884000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:122871200-122883800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:122871200-122884200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:122871600-122883800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:122871800-122881600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:122872400-122881400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:122874000-122883600	Weak transcription	Hela-S3	cervix

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