Variant report

Variant	rs17695872
Chromosome Location	chr2:20178086-20178087
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20178022-20178094	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20171001..20173873-chr2:20178005..20179964,2	K562	blood:
2	chr2:20169846..20175848-chr2:20176195..20180875,7	K562	blood:
3	chr2:20176121..20179659-chr2:20189446..20191255,3	MCF-7	breast:
4	chr2:20149305..20151850-chr2:20176525..20178682,2	MCF-7	breast:
5	chr2:20155843..20157988-chr2:20175935..20178784,2	K562	blood:

Variant related genes	Relation type
WDR35	TF binding region
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1056233	0.94[CEU][hapmap];0.92[GIH][hapmap]
rs1115275	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11680554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11681705	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11683973	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11688098	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11693384	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs11694821	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs12986437	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12988913	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12990087	0.94[CEU][hapmap];0.92[GIH][hapmap];0.80[EUR][1000 genomes]
rs12995324	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12996974	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs13001254	0.80[EUR][1000 genomes]
rs13005512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13011870	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13035048	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1370585	0.94[CEU][hapmap];0.92[GIH][hapmap]
rs16987220	0.94[CEU][hapmap]
rs16987257	0.94[CEU][hapmap];0.92[GIH][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1921731	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1992167	0.80[EUR][1000 genomes]
rs2028208	0.94[CEU][hapmap];0.92[GIH][hapmap];0.87[AMR][1000 genomes]
rs28452699	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34400777	0.94[CEU][hapmap];0.92[GIH][hapmap];0.84[AMR][1000 genomes]
rs34425205	0.80[EUR][1000 genomes]
rs34459327	0.80[EUR][1000 genomes]
rs34595677	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34741640	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35307726	0.84[AMR][1000 genomes]
rs35425971	0.82[EUR][1000 genomes]
rs35973216	0.80[EUR][1000 genomes]
rs4294960	0.94[CEU][hapmap];0.92[GIH][hapmap];0.80[EUR][1000 genomes]
rs66482567	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs66496755	0.80[AMR][1000 genomes]
rs6706311	0.84[AMR][1000 genomes]
rs6720011	0.94[CEU][hapmap]
rs67653248	0.80[EUR][1000 genomes]
rs67724270	0.84[AMR][1000 genomes]
rs67915887	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs721932	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs721933	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73214266	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs957614	0.94[CEU][hapmap];0.92[GIH][hapmap]

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	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1067839	chr2:20177392-20180238	Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
4	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
5	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
11	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:20138600-20184800	Weak transcription	Aorta	Aorta
15	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:20153200-20184400	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:20157800-20187200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20160600-20181200	Strong transcription	A549	lung
19	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:20164600-20187000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
24	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:20165000-20181600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:20165000-20187000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:20165000-20188400	Weak transcription	K562	blood
28	chr2:20165400-20187600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:20165600-20184600	Weak transcription	Gastric	stomach
30	chr2:20165800-20179800	Weak transcription	Fetal Thymus	thymus
31	chr2:20165800-20184600	Weak transcription	Lung	lung
32	chr2:20165800-20188200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:20169000-20179200	Weak transcription	Ovary	ovary
34	chr2:20169000-20184800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:20169000-20188800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:20169000-20189000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:20169200-20188800	Weak transcription	Right Ventricle	heart
38	chr2:20171000-20181800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:20171000-20182200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:20171800-20187800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:20172000-20188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:20172200-20180600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:20172800-20181600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:20173000-20182000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr2:20173000-20182000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:20173200-20178600	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:20173200-20178800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:20173200-20179400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:20173200-20180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:20173200-20181000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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