Variant report

Variant	rs16833728
Chromosome Location	chr1:151945779-151945780
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151941976..151947771-chr1:152006202..152009564,7	MCF-7	breast:
2	chr1:151890104..151891897-chr1:151945321..151946956,2	K562	blood:
3	chr1:151940762..151943209-chr1:151945501..151947443,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1038747	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10494270	0.90[CHB][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs10788817	0.81[CHB][hapmap]
rs10788820	0.81[CHB][hapmap]
rs11204915	0.81[CHB][hapmap]
rs11204919	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204920	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204922	0.86[CHB][hapmap]
rs11582739	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083193	0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12095483	0.90[ASN][1000 genomes]
rs12116923	0.86[CHB][hapmap]
rs1387833	0.86[CHB][hapmap]
rs1532133	0.81[CHB][hapmap]
rs16833668	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833669	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833670	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833743	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1844543	0.88[ASN][1000 genomes]
rs1979637	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2279501	0.91[CHB][hapmap]
rs2279502	0.91[CHB][hapmap]
rs2337685	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2337686	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338019	0.91[CHB][hapmap]
rs2338206	0.85[ASN][1000 genomes]
rs28415528	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932570	0.81[CHB][hapmap]
rs2932579	0.86[CHB][hapmap]
rs2932580	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932590	0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs2999526	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs2999528	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs2999531	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs2999534	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs2999539	0.84[TSI][hapmap]
rs2999542	0.81[CHB][hapmap]
rs2999544	0.81[CHB][hapmap]
rs3007670	0.81[CHB][hapmap]
rs3007685	0.81[CHB][hapmap]
rs3007708	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs3007711	0.81[CHB][hapmap]
rs34251437	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3791153	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845719	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56000812	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56078223	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56170235	0.85[ASN][1000 genomes]
rs56313205	0.86[ASN][1000 genomes]
rs57674198	0.85[ASN][1000 genomes]
rs57785325	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58087484	0.85[ASN][1000 genomes]
rs61814883	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61817695	0.85[ASN][1000 genomes]
rs61817697	0.83[ASN][1000 genomes]
rs61817719	0.88[ASN][1000 genomes]
rs61817720	0.88[ASN][1000 genomes]
rs61817722	0.96[ASN][1000 genomes]
rs61817723	0.94[ASN][1000 genomes]
rs61817724	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61817725	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587632	0.88[ASN][1000 genomes]
rs6587633	0.88[ASN][1000 genomes]
rs6587634	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587640	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657658	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659662	0.83[ASN][1000 genomes]
rs6662602	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6662611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662728	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663064	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6672064	0.84[ASN][1000 genomes]
rs6675930	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678672	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6682605	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684114	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684312	0.81[MEX][hapmap];0.88[TSI][hapmap]
rs6686874	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]
rs6691212	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693388	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693396	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693901	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695324	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701374	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6703448	0.88[ASN][1000 genomes]
rs6703465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694840	0.86[ASN][1000 genomes]
rs7535002	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7538652	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554832	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554859	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902313	1.00[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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971887	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943221	0.91[CHB][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9943251	0.81[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs16833728	ADAMTSL4	cis	cerebellum	SCAN
rs16833728	LCE2D	cis	parietal	SCAN
rs16833728	THEM4	cis	parietal	SCAN
rs16833728	S100A10	cis	multi-tissue	Pritchard
rs16833728	S100A10	cis	lymphoblastoid	seeQTL
rs16833728	S100A10	cis	cerebellum	SCAN
rs16833728	S100A10	cis	parietal	SCAN
rs16833728	LCE2C	cis	cerebellum	SCAN
rs16833728	NBPF18P	cis	Nerve Tibial	GTEx
rs16833728	THEM4	cis	lymphoblastoid	seeQTL
rs16833728	THEM4	cis	cerebellum	SCAN
rs16833728	THEM4	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151938400-151946200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:151939600-151950800	Enhancers	Fetal Intestine Small	intestine
4	chr1:151941000-151946200	Weak transcription	Colonic Mucosa	Colon
5	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:151941200-151952800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:151941200-151952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:151941400-151947200	Weak transcription	Liver	Liver
15	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:151941800-151949400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:151941800-151953000	Weak transcription	Lung	lung
18	chr1:151941800-151953600	Weak transcription	Gastric	stomach
19	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
20	chr1:151942400-151951800	Enhancers	Fetal Intestine Large	intestine
21	chr1:151942600-151945800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:151942600-151946800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:151943000-151949400	Weak transcription	Esophagus	oesophagus
24	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
25	chr1:151943400-151949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:151943800-151946000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:151944200-151946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:151944600-151946000	Enhancers	HSMM	muscle
29	chr1:151944800-151946000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:151944800-151946000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:151944800-151946200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:151944800-151946200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr1:151944800-151946600	Enhancers	Fetal Kidney	kidney
34	chr1:151945000-151945800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr1:151945000-151945800	Enhancers	NHLF	lung
36	chr1:151945000-151946000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:151945000-151946000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:151945000-151946000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:151945000-151946000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr1:151945000-151946000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:151945000-151946000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:151945000-151946000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:151945000-151946000	Enhancers	Small Intestine	intestine
44	chr1:151945000-151946000	Flanking Active TSS	Hela-S3	cervix
45	chr1:151945000-151946200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:151945000-151946200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:151945000-151946200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:151945000-151946200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:151945000-151946200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:151945000-151946400	Enhancers	Fetal Brain Male	brain

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