Variant report

Variant	rs16823101
Chromosome Location	chr1:184365197-184365198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184348610..184350155-chr1:184363065..184365309,2	K562	blood:
2	chr1:184363242..184365828-chrX:46987261..46989284,2	MCF-7	breast:
3	chr1:184355502..184358057-chr1:184363733..184366912,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271387	Chromatin interaction
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10489721	0.83[CEU][hapmap]
rs10489722	0.83[CEU][hapmap]
rs10494580	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10737252	0.87[ASN][1000 genomes]
rs10752936	0.88[ASN][1000 genomes]
rs10752937	0.89[ASN][1000 genomes]
rs10797963	0.93[EUR][1000 genomes]
rs10911589	0.89[ASN][1000 genomes]
rs10911590	0.89[ASN][1000 genomes]
rs10911591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10911592	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10911593	1.00[CEU][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs10911594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029316	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12048492	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12058294	1.00[CEU][hapmap]
rs12063636	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12070712	1.00[CEU][hapmap]
rs12070787	0.81[ASN][1000 genomes]
rs12085285	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12088034	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12117332	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16823097	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs16823149	1.00[CEU][hapmap]
rs1884201	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884202	0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884203	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207523	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4233119	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4326589	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4384189	0.88[ASN][1000 genomes]
rs4478778	0.83[ASN][1000 genomes]
rs4512607	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4518858	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4631655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4991700	0.89[ASN][1000 genomes]
rs4991701	0.85[EUR][1000 genomes]
rs4991703	0.86[ASN][1000 genomes]
rs57073878	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61502552	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61823500	0.93[EUR][1000 genomes]
rs61823501	0.93[EUR][1000 genomes]
rs6424948	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6424949	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6424950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6670803	0.82[EUR][1000 genomes]
rs6678278	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6688074	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691784	0.84[AMR][1000 genomes]
rs6692317	0.87[ASN][1000 genomes]
rs6696161	1.00[CEU][hapmap]
rs6696270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6700709	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs732959	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7367466	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs7415961	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512260	0.92[EUR][1000 genomes]
rs7512266	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7522628	0.83[CEU][hapmap]
rs7538587	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7548074	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv3821	chr1:184319543-184365236	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16823101	NCRNA00272	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184358000-184373400	Weak transcription	Ovary	ovary
2	chr1:184358200-184372200	Weak transcription	Fetal Kidney	kidney
3	chr1:184358200-184374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:184358400-184378200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:184359000-184368600	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:184359000-184382800	Weak transcription	Fetal Stomach	stomach
7	chr1:184359400-184377000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:184359600-184365600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:184359600-184371800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:184359600-184377000	Weak transcription	A549	lung
11	chr1:184359600-184391200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:184359800-184366400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:184360200-184371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:184360600-184367200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:184360600-184386200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:184360800-184368200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:184362400-184374800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:184362600-184365200	Weak transcription	Small Intestine	intestine
19	chr1:184362600-184368200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:184362600-184368400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:184362600-184368600	Weak transcription	Right Ventricle	heart
22	chr1:184362600-184374000	Weak transcription	Esophagus	oesophagus
23	chr1:184362600-184374400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:184362600-184377000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:184362600-184386200	Weak transcription	Lung	lung
26	chr1:184362800-184374200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:184363200-184365400	Enhancers	NHEK	skin
28	chr1:184363200-184367600	Enhancers	Psoas Muscle	Psoas
29	chr1:184363600-184365200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:184363600-184368000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:184363600-184368800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:184363800-184368600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:184364000-184365400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:184364000-184368600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:184364200-184365600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:184364200-184367000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:184364200-184368600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:184364200-184372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:184364600-184365400	Enhancers	Fetal Heart	heart
40	chr1:184364600-184366200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:184364800-184365400	Enhancers	Colon Smooth Muscle	Colon
42	chr1:184364800-184367200	Weak transcription	Left Ventricle	heart
43	chr1:184364800-184373600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:184365000-184367000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:184365000-184367200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:184365000-184368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:184365000-184368600	Weak transcription	HMEC	breast
48	chr1:184365000-184371800	Weak transcription	Right Atrium	heart
49	chr1:184365000-184378200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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