Variant report

Variant	rs6556838
Chromosome Location	chr5:93197031-93197032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0825-1	chr5:93196375-93199531	ENSG00000251023.1

Extended variants
information (count: 130 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036829	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10038828	1.00[JPT][hapmap]
rs10038831	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10041792	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10050364	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10052662	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs10053405	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10054790	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs10054903	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs10055340	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10055741	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10056879	1.00[JPT][hapmap]
rs10057130	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10057664	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs10058331	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs10060160	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10060331	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10061069	0.89[CEU][hapmap]
rs10062711	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10064368	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10065056	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10066323	0.87[MKK][hapmap];0.84[YRI][hapmap]
rs10066791	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10067541	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10071040	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs10075217	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10078194	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10078941	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs10079708	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs10214278	0.86[JPT][hapmap]
rs1026279	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1026280	0.84[YRI][hapmap]
rs1031422	1.00[YRI][hapmap]
rs1031424	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1038686	0.83[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs10476520	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10476588	0.81[YRI][hapmap]
rs10476590	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10476596	0.85[CHD][hapmap]
rs10476597	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10476598	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs10514378	0.87[MKK][hapmap];0.84[YRI][hapmap]
rs10866760	0.82[TSI][hapmap]
rs11135394	0.89[CEU][hapmap];0.90[TSI][hapmap]
rs11135397	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11948511	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12054831	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12109629	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs12153501	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12188163	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12653528	1.00[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];0.94[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs12716453	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12716454	1.00[CHD][hapmap];0.88[JPT][hapmap]
rs13154650	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13155452	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13156202	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13156865	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs13161885	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs13164315	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13167027	0.89[CEU][hapmap];0.90[TSI][hapmap]
rs13170509	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs13171131	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13357713	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13361613	0.86[CHB][hapmap]
rs1349711	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs1453003	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1470150	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs17083377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs17083380	0.89[CEU][hapmap];0.90[TSI][hapmap]
rs17312456	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17314762	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17314797	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs17314825	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs17372057	0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17372615	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17372649	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17372725	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17374166	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17374627	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1869277	1.00[YRI][hapmap]
rs1901736	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1982439	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2043979	0.89[CEU][hapmap]
rs2045019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs2045020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs2045021	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2084916	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2290937	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2924374	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs2924375	0.87[LWK][hapmap];0.81[MKK][hapmap]
rs2924377	0.82[LWK][hapmap]
rs4380636	0.87[MKK][hapmap];0.96[YRI][hapmap]
rs4607342	0.87[MKK][hapmap];0.96[YRI][hapmap]
rs6556833	0.89[CEU][hapmap]
rs6556834	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6556839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6859757	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6865441	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6874223	0.84[YRI][hapmap]
rs6874766	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6877030	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6877616	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6879620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6881815	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6890998	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6893023	0.85[MKK][hapmap];0.96[YRI][hapmap]
rs6895356	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6898507	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7701011	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7701974	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7702348	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7702649	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7713956	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7715562	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7717718	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7721668	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs7734897	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7735009	0.83[CEU][hapmap]
rs7736620	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7736892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs896729	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs9314086	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9314089	0.82[LWK][hapmap]
rs9314092	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs9314093	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs9885329	0.86[CHB][hapmap]

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	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv830405	chr5:93086825-93258518	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882384	chr5:93136661-93380123	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93162000-93215000	Weak transcription	Aorta	Aorta
2	chr5:93174400-93216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:93177400-93209200	Weak transcription	Gastric	stomach
4	chr5:93180800-93203600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:93181200-93223400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:93181400-93204000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:93181400-93222600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:93181400-93231200	Weak transcription	Adipose Nuclei	Adipose
9	chr5:93181600-93222000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:93182000-93222600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:93185000-93211400	Weak transcription	Thymus	Thymus
12	chr5:93187000-93199600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:93190800-93212000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:93191600-93211600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:93191800-93209400	Weak transcription	Brain Angular Gyrus	brain
16	chr5:93192000-93199000	Weak transcription	Placenta	Placenta
17	chr5:93192600-93222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:93193400-93220800	Weak transcription	Liver	Liver
19	chr5:93194000-93219400	Weak transcription	Fetal Lung	lung
20	chr5:93194200-93200200	Weak transcription	HSMMtube	muscle
21	chr5:93194200-93201600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:93194200-93202400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:93194200-93209400	Weak transcription	Ovary	ovary
24	chr5:93194200-93210000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:93194200-93222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:93194200-93307600	Weak transcription	Left Ventricle	heart
27	chr5:93194400-93203200	Weak transcription	Fetal Intestine Large	intestine
28	chr5:93194400-93204200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:93194400-93206000	Weak transcription	Primary B cells from cord blood	blood
30	chr5:93194400-93212000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:93194400-93212800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:93194400-93213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:93194400-93214800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:93194400-93222400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:93194400-93222400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:93194400-93222600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:93194400-93232800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:93194600-93201200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:93194600-93209400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:93195600-93204000	Weak transcription	Primary T cells from cord blood	blood
41	chr5:93195600-93222200	Weak transcription	Dnd41	blood
42	chr5:93195800-93222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:93196000-93207600	Weak transcription	Fetal Intestine Small	intestine
44	chr5:93196200-93222600	Weak transcription	Primary hematopoietic stem cells	blood

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