Variant report

Variant	rs7956548
Chromosome Location	chr12:12337813-12337814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12315377..12318046-chr12:12335015..12337960,2	K562	blood:
2	chr12:12336035..12338491-chr12:12459842..12461495,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10431302	0.86[GIH][hapmap];0.82[TSI][hapmap]
rs10492120	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10743980	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs10772536	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10772537	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10772540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10772542	0.90[CHB][hapmap];0.80[CHD][hapmap]
rs10772547	0.90[CHB][hapmap]
rs10845489	0.93[CEU][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10845491	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10845492	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845495	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10845501	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054718	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11054721	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11054724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054731	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11054744	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11609634	0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12366664	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17819999	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1819871	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284396	0.93[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2302684	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417085	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2417086	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4477532	0.93[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4763785	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61920859	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6488507	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7294695	0.93[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7302808	0.81[EUR][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7956971	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7966410	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7973531	0.90[CHB][hapmap]
rs7979447	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9705600	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7956548	LRP6	cis	parietal	SCAN
rs7956548	CLEC2A	cis	parietal	SCAN
rs7956548	AICDA	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:12288200-12342800	Weak transcription	K562	blood
5	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
9	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
11	chr12:12315400-12340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:12315400-12371600	Weak transcription	Lung	lung
13	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:12325800-12341000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:12328400-12339800	Weak transcription	Ovary	ovary
16	chr12:12328600-12339000	Weak transcription	Fetal Intestine Small	intestine
17	chr12:12329600-12343200	Weak transcription	Placenta	Placenta
18	chr12:12330200-12343200	Weak transcription	GM12878-XiMat	blood
19	chr12:12334000-12338600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:12334200-12350800	Weak transcription	Fetal Thymus	thymus
21	chr12:12334400-12338800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:12334400-12339200	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:12334400-12339800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:12334400-12343200	Weak transcription	Fetal Intestine Large	intestine
25	chr12:12334400-12348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:12334400-12349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:12334400-12349600	Weak transcription	Dnd41	blood
28	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:12334600-12349200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:12334800-12346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:12335200-12352000	Weak transcription	HSMM	muscle
36	chr12:12335200-12365800	Weak transcription	NHEK	skin
37	chr12:12335600-12338400	Enhancers	Fetal Brain Female	brain
38	chr12:12335800-12343600	Weak transcription	HMEC	breast
39	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
40	chr12:12336000-12338000	Genic enhancers	HepG2	liver
41	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
43	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:12336200-12338400	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:12336200-12339200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:12336200-12339600	Weak transcription	Psoas Muscle	Psoas
47	chr12:12336200-12340600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:12336200-12343000	Weak transcription	Brain Substantia Nigra	brain
49	chr12:12336200-12343200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:12336200-12343400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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