Variant report

Variant	rs821400
Chromosome Location	chr1:86120024-86120025
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	chr1:86114750..86117708-chr1:86118928..86121953,3	MCF-7	breast:
2	chr1:86048276..86051402-chr1:86117655..86121071,4	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10747323	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10747324	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs10873711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10873718	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs10873719	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs1094353	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1094360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037294	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405017	0.87[CHD][hapmap]
rs12410234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12756841	0.92[EUR][1000 genomes]
rs12757797	0.87[YRI][hapmap]
rs12758966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360239	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1481200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1617458	0.85[ASN][1000 genomes]
rs17128293	0.92[ASN][1000 genomes]
rs1764287	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1764295	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]
rs1775985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775987	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1775989	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1775991	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1775992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775993	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2014733	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014750	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs2026772	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2026773	0.81[ASW][hapmap]
rs2026774	0.93[ASW][hapmap];1.00[CHD][hapmap];0.87[YRI][hapmap]
rs2389973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389974	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389975	1.00[EUR][1000 genomes]
rs2773131	0.83[AFR][1000 genomes]
rs2785082	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2970548	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313723	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs313724	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs313725	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs369999	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs381453	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs383558	0.96[EUR][1000 genomes]
rs399547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs401657	0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs420515	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs425357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs429040	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs430956	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs432254	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs4379699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs438401	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs444875	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450953	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs4949913	0.82[YRI][hapmap]
rs4949917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4949918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6673975	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs6682235	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs6686719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7521240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528385	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7529942	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7533395	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7535884	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7547023	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7554621	0.92[EUR][1000 genomes]
rs821377	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821378	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821382	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821383	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821385	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821390	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821402	0.93[ASW][hapmap]
rs821403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs849158	0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324152	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9324153	0.93[ASW][hapmap]
rs9651138	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9661608	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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661951	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]
rs9701898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793556	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];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs821400	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
3	chr1:86103600-86120200	Weak transcription	HMEC	breast
4	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
5	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:86103600-86172600	Weak transcription	Gastric	stomach
11	chr1:86106000-86141200	Weak transcription	Lung	lung
12	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:86114200-86120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
17	chr1:86115200-86123400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:86115200-86124800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
20	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:86116000-86123400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:86116400-86120200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:86116400-86127000	Weak transcription	Fetal Kidney	kidney
25	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:86116600-86120200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:86116600-86121800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:86116600-86122200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:86116600-86123600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:86116600-86129200	Weak transcription	Aorta	Aorta
32	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
34	chr1:86116800-86124600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
36	chr1:86117200-86120600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:86117400-86122000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:86117400-86122400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:86117400-86122800	Strong transcription	Dnd41	blood
40	chr1:86117400-86123200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
42	chr1:86117800-86120400	Strong transcription	Liver	Liver
43	chr1:86117800-86121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:86117800-86121000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:86117800-86122200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:86117800-86122800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:86118000-86120800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:86118600-86120600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:86118600-86121000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:86118600-86121800	Strong transcription	Primary T cells fromperipheralblood	blood

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