Variant report

Variant	rs11693384
Chromosome Location	chr2:20149417-20149418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20147964..20150748-chr2:20153485..20156219,3	K562	blood:
2	chr2:20147509..20150475-chr2:20183236..20185493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1056233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1115275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11680554	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11681705	0.89[CEU][hapmap]
rs11683973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688098	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11688680	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11694821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986437	0.89[CEU][hapmap]
rs12988913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12996974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13005512	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs13006748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13011870	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13035048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370585	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16987220	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16987257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695872	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1921731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992167	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34400777	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34425205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34459327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35307726	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35425971	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35973216	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4294960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66496755	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6706311	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67653248	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67724270	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs721932	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721933	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73214266	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs957614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
6	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
7	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
8	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:20130400-20164600	Weak transcription	Lung	lung
11	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:20130600-20161200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:20133600-20164800	Weak transcription	Gastric	stomach
16	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
17	chr2:20133800-20151600	Weak transcription	Fetal Kidney	kidney
18	chr2:20133800-20173200	Weak transcription	NHEK	skin
19	chr2:20133800-20176800	Weak transcription	HMEC	breast
20	chr2:20134200-20168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:20136400-20150800	Weak transcription	Thymus	Thymus
22	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
23	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:20136600-20151600	Weak transcription	Brain Germinal Matrix	brain
25	chr2:20136600-20171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:20136800-20171400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:20137600-20150000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:20137600-20161000	Weak transcription	HSMMtube	muscle
32	chr2:20137600-20165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:20137800-20152000	Weak transcription	Brain Anterior Caudate	brain
34	chr2:20137800-20161200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:20137800-20165000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:20138000-20165000	Weak transcription	Fetal Brain Female	brain
37	chr2:20138000-20177000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:20138200-20152000	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:20138200-20164200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:20138200-20165000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:20138200-20165000	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:20138200-20171400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:20138400-20164400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:20138400-20167800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:20138600-20152000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:20138600-20165000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:20138600-20165000	Weak transcription	Left Ventricle	heart
49	chr2:20138600-20165400	Weak transcription	Osteobl	bone
50	chr2:20138600-20184800	Weak transcription	Aorta	Aorta

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