Variant report

Variant	rs6686874
Chromosome Location	chr1:151915740-151915741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151913842..151916280-chr1:151933238..151936084,3	MCF-7	breast:
2	chr1:151914726..151916924-chr1:151917247..151919609,3	MCF-7	breast:
3	chr1:151912762..151919992-chr1:151963219..151969467,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1038747	0.89[CHB][hapmap]
rs10494270	0.91[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788817	0.86[CHB][hapmap]
rs10788820	0.86[CHB][hapmap]
rs11204906	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11204915	0.86[CHB][hapmap]
rs11204919	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11204920	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11204922	0.81[CHB][hapmap]
rs11582739	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12064020	0.80[YRI][hapmap]
rs12083193	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12095483	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116923	0.90[CHB][hapmap]
rs12566232	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1387833	0.91[CHB][hapmap]
rs16828432	0.80[YRI][hapmap]
rs16833610	0.80[YRI][hapmap]
rs16833668	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833669	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833670	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833728	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16833743	0.86[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844543	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979637	0.80[CHB][hapmap]
rs2279501	0.95[CHB][hapmap]
rs2279502	0.95[CHB][hapmap];0.83[TSI][hapmap]
rs2337685	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337686	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337687	0.80[YRI][hapmap]
rs2338019	0.86[CHB][hapmap]
rs2338206	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28415528	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932579	0.91[CHB][hapmap];0.80[TSI][hapmap]
rs2932580	0.96[ASN][1000 genomes]
rs2932590	0.91[CHB][hapmap];0.80[TSI][hapmap]
rs2999526	0.91[CHB][hapmap];0.81[TSI][hapmap]
rs2999528	0.91[CHB][hapmap];0.81[TSI][hapmap]
rs2999531	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs2999542	0.86[CHB][hapmap]
rs2999544	0.86[CHB][hapmap];0.82[TSI][hapmap]
rs3007670	0.86[CHB][hapmap]
rs3007685	0.86[CHB][hapmap]
rs3007708	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs3007711	0.86[CHB][hapmap]
rs34251437	0.87[ASN][1000 genomes]
rs3791153	0.86[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845713	0.84[CHB][hapmap]
rs4845719	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56000812	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56028913	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56078223	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56170235	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56313205	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57674198	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57785325	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58087484	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61814883	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61817695	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817697	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817719	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817720	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817722	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817723	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61817724	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817725	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587632	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587633	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587634	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587635	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587636	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587637	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587638	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587640	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs6657658	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6659662	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6662602	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662611	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6662728	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6663064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672064	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6675930	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678672	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682605	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684114	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684312	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	0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6691212	0.87[ASN][1000 genomes]
rs6693388	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693396	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693901	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695324	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701374	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703448	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703465	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72694840	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532162	0.80[YRI][hapmap]
rs7533854	0.80[YRI][hapmap]
rs7535002	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538652	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541099	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7554832	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7554859	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902313	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs971887	0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9943221	0.91[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9943251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][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	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
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6686874	THEM4	cis	cerebellum	SCAN
rs6686874	THEM4	cis	multi-tissue	Pritchard
rs6686874	LCE2D	cis	parietal	SCAN
rs6686874	S100A10	cis	cerebellum	SCAN
rs6686874	S100A10	cis	multi-tissue	Pritchard
rs6686874	THEM4	cis	parietal	SCAN
rs6686874	LCE2C	cis	cerebellum	SCAN
rs6686874	S100A10	cis	parietal	SCAN
rs6686874	S100A10	cis	lymphoblastoid	seeQTL
rs6686874	THEM4	cis	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151907000-151917400	Weak transcription	Right Atrium	heart
2	chr1:151907600-151916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:151908200-151916600	Weak transcription	Placenta	Placenta
4	chr1:151908200-151917000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:151909400-151916800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:151909400-151917000	Weak transcription	Colonic Mucosa	Colon
7	chr1:151909600-151917800	Weak transcription	HUVEC	blood vessel
8	chr1:151909800-151916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:151911600-151916000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:151912000-151917000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:151912200-151917800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:151913000-151917200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:151913000-151919800	Enhancers	Fetal Intestine Large	intestine
14	chr1:151913200-151916600	Enhancers	Hela-S3	cervix
15	chr1:151913200-151916800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:151913200-151917800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:151913200-151919000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:151913800-151917000	Enhancers	Adipose Nuclei	Adipose
19	chr1:151914000-151916000	Weak transcription	Left Ventricle	heart
20	chr1:151914000-151916600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:151914000-151917000	Weak transcription	Esophagus	oesophagus
22	chr1:151914000-151917000	Weak transcription	Psoas Muscle	Psoas
23	chr1:151914000-151917000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:151914000-151917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:151914000-151922000	Weak transcription	Spleen	Spleen
26	chr1:151914200-151916800	Weak transcription	HSMM	muscle
27	chr1:151914200-151917000	Weak transcription	Pancreas	Pancrea
28	chr1:151914200-151917400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:151914200-151917800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:151914400-151916400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:151914400-151916800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:151914400-151917000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:151914400-151917200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:151914400-151917200	Weak transcription	HSMMtube	muscle
35	chr1:151914600-151916600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:151914600-151916600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:151914600-151916600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:151914600-151916600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:151914600-151916800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:151914600-151917000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:151914600-151917400	Weak transcription	Aorta	Aorta
42	chr1:151914600-151918000	Weak transcription	Osteobl	bone
43	chr1:151914800-151916000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:151914800-151916600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:151914800-151916600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:151914800-151916600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:151914800-151916600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:151914800-151916600	Weak transcription	Stomach Mucosa	stomach
49	chr1:151914800-151916800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:151914800-151916800	Weak transcription	HMEC	breast

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