Variant report

Variant	rs16833668
Chromosome Location	chr1:151918164-151918165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151911549..151914753-chr1:151917047..151920046,3	K562	blood:
2	chr1:151918122..151918743-chr3:39041388..39042072,2	MCF-7	breast:
3	chr1:151881300..151883232-chr1:151916135..151919010,3	K562	blood:
4	chr1:151914726..151916924-chr1:151917247..151919609,3	MCF-7	breast:
5	chr1:151915835..151920651-chr1:152004121..152010886,7	MCF-7	breast:
6	chr1:151917183..151919501-chr1:152008114..152010423,2	K562	blood:
7	chr1:151912468..151914672-chr1:151915878..151918537,2	MCF-7	breast:
8	chr1:151880767..151883017-chr1:151916135..151918351,3	K562	blood:
9	chr1:151902230..151904695-chr1:151916029..151918681,2	K562	blood:
10	chr1:151912762..151919992-chr1:151963219..151969467,12	MCF-7	breast:
11	chr1:151917185..151918906-chr1:151960945..151963030,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1038747	0.89[CHB][hapmap]
rs10494270	0.95[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788817	0.86[CHB][hapmap]
rs10788820	0.86[CHB][hapmap]
rs11204906	0.85[AMR][1000 genomes]
rs11204915	0.86[CHB][hapmap]
rs11204919	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204920	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204922	0.81[CHB][hapmap]
rs11582739	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12083193	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs12095483	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116923	0.90[CHB][hapmap]
rs12566232	0.82[AMR][1000 genomes]
rs1387833	0.91[CHB][hapmap]
rs16833669	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833670	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833728	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]
rs16833743	0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1844543	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979637	0.80[CHB][hapmap]
rs2279501	0.95[CHB][hapmap]
rs2279502	0.95[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2337685	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337686	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338019	0.86[CHB][hapmap]
rs2338206	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28415528	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932579	0.91[CHB][hapmap]
rs2932580	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932590	0.91[CHB][hapmap]
rs2999526	0.91[CHB][hapmap]
rs2999528	0.91[CHB][hapmap]
rs2999531	0.86[CHB][hapmap]
rs2999542	0.86[CHB][hapmap]
rs2999544	0.86[CHB][hapmap]
rs3007670	0.86[CHB][hapmap]
rs3007685	0.86[CHB][hapmap]
rs3007708	0.86[CHB][hapmap]
rs3007711	0.86[CHB][hapmap]
rs34251437	0.87[ASN][1000 genomes]
rs3791153	0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4845713	0.84[CHB][hapmap]
rs4845719	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56000812	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56028913	0.80[AMR][1000 genomes]
rs56078223	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56170235	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56313205	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57674198	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57785325	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58087484	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61814883	0.85[ASN][1000 genomes]
rs61817695	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817697	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817719	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817720	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817722	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817723	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61817724	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817725	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587632	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587633	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587634	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587635	0.87[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587636	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587637	0.86[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587638	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587640	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6657658	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659662	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6662602	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662611	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662728	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672064	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6675930	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678672	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6682605	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684114	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684312	0.85[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes]
rs6686874	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]
rs6690449	0.87[AMR][1000 genomes]
rs6691212	0.87[ASN][1000 genomes]
rs6693388	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693396	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693901	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695324	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701374	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703448	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703465	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72694840	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538652	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541099	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554832	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554859	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs902313	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971887	0.83[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943221	0.95[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9943251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs16833668	LCE2D	cis	parietal	SCAN
rs16833668	S100A10	cis	multi-tissue	Pritchard
rs16833668	S100A10	cis	parietal	SCAN
rs16833668	THEM4	cis	lymphoblastoid	seeQTL
rs16833668	THEM4	cis	multi-tissue	Pritchard
rs16833668	SCNM1	cis	parietal	SCAN
rs16833668	S100A10	cis	cerebellum	SCAN
rs16833668	PGLYRP3	cis	parietal	SCAN
rs16833668	TCHHL1	cis	parietal	SCAN
rs16833668	LCE2C	cis	cerebellum	SCAN
rs16833668	THEM4	cis	cerebellum	SCAN
rs16833668	THEM4	cis	parietal	SCAN
rs16833668	S100A13	cis	parietal	SCAN
rs16833668	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151913000-151919800	Enhancers	Fetal Intestine Large	intestine
2	chr1:151913200-151919000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:151914000-151922000	Weak transcription	Spleen	Spleen
4	chr1:151915200-151919600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:151915600-151918400	Weak transcription	Ovary	ovary
6	chr1:151915600-151919400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:151916200-151919600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:151916400-151918400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:151916400-151919200	Enhancers	K562	blood
10	chr1:151916400-151919400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:151916400-151919600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:151916400-151919800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:151916600-151918200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:151916600-151918200	Flanking Active TSS	Hela-S3	cervix
15	chr1:151916600-151918600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:151916600-151919000	Enhancers	Placenta	Placenta
17	chr1:151916600-151919000	Enhancers	Small Intestine	intestine
18	chr1:151916600-151919200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:151916600-151919400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:151916600-151919400	Enhancers	Colon Smooth Muscle	Colon
21	chr1:151916600-151919600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:151916600-151919600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:151916600-151919600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:151916600-151919600	Enhancers	Fetal Muscle Leg	muscle
25	chr1:151916600-151919600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:151916600-151919600	Enhancers	Stomach Mucosa	stomach
27	chr1:151916600-151919800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:151916600-151919800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:151916600-151919800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:151916600-151919800	Enhancers	Fetal Intestine Small	intestine
31	chr1:151916800-151918200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:151916800-151918200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:151916800-151918200	Enhancers	NHEK	skin
34	chr1:151916800-151918600	Enhancers	HMEC	breast
35	chr1:151916800-151918800	Enhancers	NHDF-Ad	bronchial
36	chr1:151916800-151919000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:151916800-151919400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:151916800-151919600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:151916800-151919600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:151916800-151919800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:151916800-151919800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:151916800-151919800	Enhancers	HSMM	muscle
43	chr1:151916800-151919800	Enhancers	NHLF	lung
44	chr1:151916800-151920600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:151917000-151918400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:151917000-151919000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:151917000-151919000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:151917000-151919000	Flanking Active TSS	A549	lung
49	chr1:151917000-151919200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr1:151917000-151919400	Enhancers	Pancreatic Islets	Pancreatic Islet

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