Variant report

Variant	rs11706332
Chromosome Location	chr3:28358057-28358058
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	chr3:28303255..28306157-chr3:28357990..28360195,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMC1-3	chr3:28357824-28361253	NONHSAT088780

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1037723	0.82[ASN][1000 genomes]
rs11707705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11710963	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11712484	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11712489	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11720107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs11918050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11921692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11921943	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11924173	0.87[ASN][1000 genomes]
rs11926399	0.85[ASN][1000 genomes]
rs12107256	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs13074633	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13075840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs13080155	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13081520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13081787	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13082167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs13083544	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.85[ASN][1000 genomes]
rs13085075	1.00[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs13085245	0.86[ASN][1000 genomes]
rs13087143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13087774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13088574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs13090296	0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs13090439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13092618	0.83[ASN][1000 genomes]
rs13093242	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13095628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs13095675	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs13099152	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13101128	0.81[ASN][1000 genomes]
rs1457909	0.80[ASN][1000 genomes]
rs1457910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1585211	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1598846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap]
rs1599826	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1606386	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1606388	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1610238	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs17021221	0.85[CHB][hapmap]
rs17021306	0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs17021402	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs17357206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17638742	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17638782	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17638991	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17639978	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17695765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17695884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17696025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17696459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17696561	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17696783	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs1870259	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2016948	0.86[ASN][1000 genomes]
rs2168799	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs34017994	0.86[ASN][1000 genomes]
rs34311197	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34419916	0.86[ASN][1000 genomes]
rs34541614	0.85[ASN][1000 genomes]
rs34574968	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34748842	0.82[ASN][1000 genomes]
rs34796684	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35088087	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35137555	0.80[ASN][1000 genomes]
rs35177150	0.82[ASN][1000 genomes]
rs35217335	0.86[ASN][1000 genomes]
rs35232922	0.86[ASN][1000 genomes]
rs35439056	0.84[ASN][1000 genomes]
rs35460328	0.86[ASN][1000 genomes]
rs35496780	0.86[ASN][1000 genomes]
rs35530532	0.86[ASN][1000 genomes]
rs35565264	0.86[ASN][1000 genomes]
rs35678778	0.84[ASN][1000 genomes]
rs35702956	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35736614	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35768817	0.86[ASN][1000 genomes]
rs35825908	0.82[ASN][1000 genomes]
rs35845822	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35937120	0.84[ASN][1000 genomes]
rs36051688	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36105900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4452283	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4522735	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680909	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs4680913	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs56946005	0.84[ASN][1000 genomes]
rs58918848	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59975750	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60043893	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62250271	0.85[ASN][1000 genomes]
rs62250272	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62250273	0.84[ASN][1000 genomes]
rs62250296	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62251105	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62251108	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251131	0.89[ASN][1000 genomes]
rs62251134	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62251138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62251144	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62252069	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6551255	0.87[ASN][1000 genomes]
rs66502736	0.88[ASN][1000 genomes]
rs66716911	0.86[ASN][1000 genomes]
rs66733194	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67023418	0.86[ASN][1000 genomes]
rs6771057	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs6771460	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6803692	1.00[CHB][hapmap]
rs68085718	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs68097246	0.84[ASN][1000 genomes]
rs71087683	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7434193	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7635383	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638450	0.85[ASN][1000 genomes]
rs7639750	1.00[CHB][hapmap]
rs7641491	1.00[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs7643191	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs7649498	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs7650831	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651883	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs952888	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683360	0.82[ASN][1000 genomes]
rs969443	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9843464	1.00[CHB][hapmap];0.90[CHD][hapmap]

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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:28315000-28363000	Weak transcription	A549	lung
3	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
5	chr3:28326400-28365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:28332800-28360000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:28332800-28360200	Weak transcription	Left Ventricle	heart
8	chr3:28332800-28360400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:28332800-28362400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:28332800-28365200	Weak transcription	HSMMtube	muscle
11	chr3:28332800-28365400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:28336800-28359400	Weak transcription	K562	blood
13	chr3:28337200-28365200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:28337400-28360400	Weak transcription	Liver	Liver
15	chr3:28337400-28361000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:28337400-28363000	Weak transcription	GM12878-XiMat	blood
17	chr3:28337600-28360200	Weak transcription	Fetal Lung	lung
18	chr3:28337600-28360200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:28337600-28361000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:28338000-28359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:28338000-28360200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:28338000-28360600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:28338200-28364000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:28339600-28359200	Weak transcription	Dnd41	blood
25	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
26	chr3:28347400-28360000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:28348600-28360000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:28348600-28365200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:28349000-28365400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:28349400-28364200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:28349400-28365600	Weak transcription	Psoas Muscle	Psoas
32	chr3:28349600-28365400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:28349800-28359800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:28349800-28389400	Weak transcription	Gastric	stomach
35	chr3:28350000-28359600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:28350000-28363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:28350200-28361600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:28350400-28365400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:28350600-28360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:28351200-28366600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:28351400-28365600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:28351400-28366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:28352800-28360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:28353200-28360200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:28354200-28364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:28354800-28363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:28354800-28365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:28355200-28360600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:28355800-28359400	Weak transcription	Primary T cells fromperipheralblood	blood

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