Variant report

Variant	rs6684312
Chromosome Location	chr1:151844650-151844651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151818410..151820292-chr1:151842625..151844797,2	MCF-7	breast:
2	chr1:151843870..151847170-chr1:151852619..151855658,3	K562	blood:
3	chr1:151843139..151845993-chr1:151848350..151850912,2	K562	blood:
4	chr1:151842414..151844891-chr1:151846199..151848335,2	K562	blood:
5	chr1:151812256..151814665-chr1:151841622..151845520,3	MCF-7	breast:
6	chr1:151833646..151837340-chr1:151842785..151845741,4	MCF-7	breast:
7	chr1:151843538..151846125-chr1:151876423..151878232,2	K562	blood:

Variant related genes	Relation type
ENSG00000201134	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000234614	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10494270	0.86[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10888445	0.95[CHB][hapmap]
rs11204906	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204919	0.81[AMR][1000 genomes]
rs11204920	0.81[AMR][1000 genomes]
rs11582739	0.85[AMR][1000 genomes]
rs12064020	0.89[YRI][hapmap]
rs12083193	0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs12095483	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12566232	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13320	0.95[CHB][hapmap]
rs16828432	0.89[YRI][hapmap]
rs16833610	0.89[YRI][hapmap]
rs16833668	0.85[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes]
rs16833669	0.87[AMR][1000 genomes]
rs16833670	0.87[AMR][1000 genomes]
rs16833728	0.81[MEX][hapmap];0.88[TSI][hapmap]
rs16833743	0.82[AMR][1000 genomes]
rs1844543	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2337685	0.87[AMR][1000 genomes]
rs2337686	0.87[AMR][1000 genomes]
rs2337687	0.89[YRI][hapmap]
rs2338206	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28415528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932579	0.80[TSI][hapmap]
rs2999544	0.82[TSI][hapmap]
rs3791153	0.82[AMR][1000 genomes]
rs4845719	0.81[AMR][1000 genomes]
rs56000812	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56028913	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56078223	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56170235	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56313205	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57674198	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57785325	0.87[AMR][1000 genomes]
rs58087484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61814883	0.80[AMR][1000 genomes]
rs61817695	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61817697	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61817719	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817720	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817722	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817723	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817724	0.87[AMR][1000 genomes]
rs61817725	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6587632	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587633	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587634	0.87[AMR][1000 genomes]
rs6587640	0.88[TSI][hapmap]
rs6657658	0.81[AMR][1000 genomes]
rs6659662	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6662602	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6662611	0.81[AMR][1000 genomes]
rs6663064	1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671719	0.85[AFR][1000 genomes]
rs6672064	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6675930	0.87[AMR][1000 genomes]
rs6678672	0.86[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs6682605	0.83[AMR][1000 genomes]
rs6684114	0.87[AMR][1000 genomes]
rs6685187	0.95[CHB][hapmap]
rs6686874	0.80[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6690449	0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693388	0.87[AMR][1000 genomes]
rs6693396	0.87[AMR][1000 genomes]
rs6693901	0.87[AMR][1000 genomes]
rs6695324	0.87[AMR][1000 genomes]
rs6701374	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6703448	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6703465	0.81[AMR][1000 genomes]
rs72694840	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7523082	0.95[CHB][hapmap]
rs7532162	0.90[YRI][hapmap]
rs7533854	0.89[YRI][hapmap]
rs7535002	0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7538652	0.85[AMR][1000 genomes]
rs7541099	0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs7554832	0.81[AMR][1000 genomes]
rs7554859	0.83[AMR][1000 genomes]
rs902313	0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs971887	0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs9943221	0.86[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9943251	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6684312	LCE2C	cis	cerebellum	SCAN
rs6684312	S100A10	cis	lymphoblastoid	seeQTL
rs6684312	S100A10	cis	parietal	SCAN
rs6684312	THEM4	cis	multi-tissue	Pritchard
rs6684312	S100A10	cis	cerebellum	SCAN
rs6684312	THEM4	cis	lymphoblastoid	seeQTL
rs6684312	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs6684312	S100A10	cis	multi-tissue	Pritchard
rs6684312	THEM4	cis	cerebellum	SCAN
rs6684312	LCE2D	cis	parietal	SCAN
rs6684312	THEM4	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
2	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:151826400-151846200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151829000-151845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:151831000-151881400	Weak transcription	Ovary	ovary
6	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151832800-151846000	Weak transcription	Spleen	Spleen
8	chr1:151834000-151849600	Weak transcription	Esophagus	oesophagus
9	chr1:151835600-151847600	Weak transcription	HSMMtube	muscle
10	chr1:151837200-151845600	Weak transcription	Lung	lung
11	chr1:151837400-151846000	Weak transcription	Left Ventricle	heart
12	chr1:151837600-151845400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:151837600-151845400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:151837600-151845400	Weak transcription	Right Ventricle	heart
15	chr1:151837800-151846200	Weak transcription	Fetal Thymus	thymus
16	chr1:151839600-151845800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:151840200-151846000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:151840400-151845400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:151840400-151846000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:151840600-151846000	Weak transcription	Adipose Nuclei	Adipose
21	chr1:151840600-151864600	Weak transcription	NH-A	brain
22	chr1:151840800-151845400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:151840800-151845400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151840800-151846000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:151840800-151847600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:151840800-151857800	Weak transcription	K562	blood
27	chr1:151841000-151845800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:151841000-151846000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:151841000-151846200	Weak transcription	Fetal Lung	lung
30	chr1:151841200-151845600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:151841200-151846000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:151841200-151846200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:151841200-151847600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:151841200-151859200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:151841200-151880800	Weak transcription	NHLF	lung
36	chr1:151841400-151846000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:151841400-151860000	Weak transcription	Hela-S3	cervix
38	chr1:151841400-151860200	Weak transcription	Osteobl	bone
39	chr1:151841600-151845400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:151841600-151845400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:151841600-151864000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:151841800-151845000	Weak transcription	Fetal Kidney	kidney
43	chr1:151842000-151845200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:151842600-151846000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:151843000-151845200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:151843000-151846000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:151843000-151846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:151843000-151846000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:151843200-151845400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:151843200-151846000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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