Variant report

Variant	rs7314665
Chromosome Location	chr12:49055179-49055180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49046686..49049905-chr12:49054030..49058402,3	K562	blood:
2	chr12:49052583..49059422-chr12:49071692..49076510,9	K562	blood:
3	chr12:49052650..49057544-chr12:49071692..49076123,6	K562	blood:
4	chr12:49054189..49057394-chr12:49060673..49063657,4	K562	blood:
5	chr12:49028821..49031213-chr12:49054853..49056356,2	MCF-7	breast:
6	chr12:49049545..49052092-chr12:49054304..49056885,2	K562	blood:

Variant related genes	Relation type
ENSG00000206612	Chromatin interaction
ENSG00000221491	Chromatin interaction
ENSG00000207313	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10783273	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10783274	0.91[ASN][1000 genomes]
rs10783275	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783277	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs10783278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783281	0.81[EUR][1000 genomes]
rs10875849	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs10875850	0.88[ASN][1000 genomes]
rs10875852	0.93[ASN][1000 genomes]
rs10875853	0.93[ASN][1000 genomes]
rs10875861	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875862	0.85[ASN][1000 genomes]
rs1110432	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168657	0.86[ASN][1000 genomes]
rs11168665	0.93[ASN][1000 genomes]
rs11168674	0.90[ASN][1000 genomes]
rs11168698	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12299955	0.93[ASN][1000 genomes]
rs12426435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316514	0.84[ASN][1000 genomes]
rs1863541	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1895995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2114320	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2162317	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2277365	0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2277366	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291728	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2409085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2898087	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3209584	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35717253	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741628	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741630	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741632	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3803025	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3943899	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113946	0.88[ASN][1000 genomes]
rs4500528	0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4760735	0.88[ASN][1000 genomes]
rs4760737	0.89[ASN][1000 genomes]
rs4760739	0.96[ASN][1000 genomes]
rs4760740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580689	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580690	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580693	0.83[EUR][1000 genomes]
rs7133756	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs7138190	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138930	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs7139119	0.82[EUR][1000 genomes]
rs7139236	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299276	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7304711	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7305907	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7306604	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308699	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954446	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7954548	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7964546	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7966065	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973824	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974151	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7974625	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7975030	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7975821	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs9332441	0.94[ASN][1000 genomes]
rs9634241	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634242	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9634262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1043220	chr12:49045458-49065987	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1052256	chr12:49048506-49065987	Genic enhancers Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7314665	ZNF641	cis	cerebellum	SCAN
rs7314665	FAM186B	cis	cerebellum	SCAN
rs7314665	SNORA2B	cis	cerebellum	SCAN
rs7314665	ADCY6	cis	parietal	SCAN
rs7314665	WNT10B	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49036800-49072000	Strong transcription	Liver	Liver
2	chr12:49037800-49056600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:49037800-49072400	Strong transcription	Placenta	Placenta
4	chr12:49038200-49070800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:49038400-49060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:49038800-49071800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:49039000-49072200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:49039400-49068800	Weak transcription	Right Atrium	heart
9	chr12:49039400-49071800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:49039800-49071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:49039800-49071000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:49040000-49057000	Strong transcription	Dnd41	blood
13	chr12:49040000-49059400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:49040000-49072600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:49040400-49060600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:49040400-49072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:49041000-49071800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49041200-49061200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:49041200-49068200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr12:49041600-49065200	Weak transcription	Stomach Mucosa	stomach
21	chr12:49041800-49065200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:49041800-49070800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:49041800-49071000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:49041800-49072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine
26	chr12:49042400-49056800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:49042400-49065200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:49042400-49072800	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:49042600-49064200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:49043800-49057600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr12:49043800-49068800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:49044000-49068200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:49044200-49056600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:49044200-49057000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:49044200-49059800	Strong transcription	A549	lung
36	chr12:49044200-49071000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:49044200-49072400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:49044200-49072800	Strong transcription	Fetal Thymus	thymus
39	chr12:49044400-49056400	Strong transcription	Primary T cells from cord blood	blood
40	chr12:49044400-49056600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:49044400-49057000	Strong transcription	NHEK	skin
42	chr12:49044400-49065200	Strong transcription	Osteobl	bone
43	chr12:49044400-49071000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:49044400-49071400	Strong transcription	Thymus	Thymus
45	chr12:49044400-49072400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:49044600-49055400	Strong transcription	Brain Anterior Caudate	brain
47	chr12:49044600-49056600	Strong transcription	Adipose Nuclei	Adipose
48	chr12:49044600-49072400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:49044800-49068000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:49044800-49071200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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