Variant report

Variant	rs833820
Chromosome Location	chr12:49347819-49347820
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49346245..49347983-chr12:49448543..49450542,2	K562	blood:
2	chr12:49335548..49339838-chr12:49342673..49348492,5	K562	blood:
3	chr12:49330906..49333474-chr12:49345392..49348015,2	MCF-7	breast:
4	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
5	chr12:49346261..49349011-chr12:49376285..49379278,2	K562	blood:
6	chr12:49344320..49348348-chr12:49348662..49352888,9	MCF-7	breast:
7	chr12:49347725..49349691-chr12:49358363..49360847,2	MCF-7	breast:
8	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
9	chr12:49346973..49349302-chr12:49353615..49356127,3	K562	blood:
10	chr12:49335061..49337813-chr12:49345711..49348492,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134287	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000238395	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1051886	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1054376	0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs10747556	0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10747557	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs10747558	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs10783289	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783290	0.85[ASN][1000 genomes]
rs10783292	0.85[ASN][1000 genomes]
rs10783293	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783294	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783295	0.90[ASN][1000 genomes]
rs10783297	0.97[ASN][1000 genomes]
rs10875883	0.81[CEU][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs10875886	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875893	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875894	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875895	0.90[ASN][1000 genomes]
rs10875896	0.87[ASN][1000 genomes]
rs10875897	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875898	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875899	0.86[ASN][1000 genomes]
rs10875900	0.97[ASN][1000 genomes]
rs10875901	0.98[ASN][1000 genomes]
rs10875902	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1111662	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs11168779	0.88[ASN][1000 genomes]
rs11168783	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168784	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168785	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168790	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168792	0.92[ASN][1000 genomes]
rs11168794	0.92[ASN][1000 genomes]
rs11168795	0.96[ASN][1000 genomes]
rs11168797	0.96[ASN][1000 genomes]
rs11168798	0.91[ASN][1000 genomes]
rs11168800	0.91[ASN][1000 genomes]
rs11168801	0.91[ASN][1000 genomes]
rs11168803	0.97[ASN][1000 genomes]
rs11168811	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168812	0.97[ASN][1000 genomes]
rs11608916	0.89[ASN][1000 genomes]
rs11610459	0.90[ASN][1000 genomes]
rs11610497	0.90[ASN][1000 genomes]
rs11614474	0.90[ASN][1000 genomes]
rs12227240	0.87[ASN][1000 genomes]
rs12228521	0.89[ASN][1000 genomes]
rs12229275	0.90[ASN][1000 genomes]
rs12423542	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12579249	0.90[ASN][1000 genomes]
rs1318692	0.88[ASN][1000 genomes]
rs1690182	0.97[ASN][1000 genomes]
rs1818996	0.97[ASN][1000 genomes]
rs1830192	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2030900	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2070940	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2073480	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2131713	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2272311	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2272312	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2293449	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2368701	0.89[ASN][1000 genomes]
rs2446987	0.80[EUR][1000 genomes]
rs2447000	0.81[EUR][1000 genomes]
rs2447001	0.81[EUR][1000 genomes]
rs2453063	0.97[ASN][1000 genomes]
rs2463175	0.95[ASN][1000 genomes]
rs2641450	0.94[ASN][1000 genomes]
rs2694839	0.96[ASN][1000 genomes]
rs2694840	0.94[ASN][1000 genomes]
rs2926806	0.86[GIH][hapmap]
rs2934998	0.86[GIH][hapmap]
rs3741627	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs3759146	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782353	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs3809147	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3825182	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3825184	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs4018510	0.97[ASN][1000 genomes]
rs4237854	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4433614	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4526804	0.98[ASN][1000 genomes]
rs4760600	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760661	0.89[ASN][1000 genomes]
rs4760662	0.83[ASN][1000 genomes]
rs4760663	0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs4760664	0.98[ASN][1000 genomes]
rs4760665	0.89[ASN][1000 genomes]
rs4760666	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760667	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4760668	0.97[ASN][1000 genomes]
rs58023472	0.90[ASN][1000 genomes]
rs59087236	0.98[ASN][1000 genomes]
rs61941142	0.88[ASN][1000 genomes]
rs61942166	0.94[ASN][1000 genomes]
rs61942167	0.96[ASN][1000 genomes]
rs61942169	0.97[ASN][1000 genomes]
rs61942207	0.98[ASN][1000 genomes]
rs61942209	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580696	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs7297958	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7298330	0.90[ASN][1000 genomes]
rs7304942	0.90[ASN][1000 genomes]
rs7313988	0.98[ASN][1000 genomes]
rs7489036	0.84[ASN][1000 genomes]
rs7963018	0.97[ASN][1000 genomes]
rs7963160	0.96[ASN][1000 genomes]
rs7976473	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs833476	0.81[CEU][hapmap]
rs833821	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833822	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs833827	0.98[ASN][1000 genomes]
rs833828	0.96[ASN][1000 genomes]
rs833839	0.91[ASN][1000 genomes]
rs833840	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833841	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs833842	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833843	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs961320	0.88[ASN][1000 genomes]
rs9645813	0.91[ASN][1000 genomes]
rs9783452	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9783477	0.98[ASN][1000 genomes]
rs9788029	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9795742	0.88[ASN][1000 genomes]
rs9796008	0.90[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs833820	ADCY6	cis	parietal	SCAN
rs833820	AQP2	cis	parietal	SCAN
rs833820	FKBP11	cis	parietal	SCAN
rs833820	FKBP11	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49319800-49349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:49329400-49349400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:49330800-49349000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:49332000-49349000	Weak transcription	Stomach Mucosa	stomach
6	chr12:49333800-49349400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:49334800-49348000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:49334800-49348600	Weak transcription	Small Intestine	intestine
9	chr12:49334800-49349400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:49334800-49349800	Weak transcription	Psoas Muscle	Psoas
11	chr12:49335000-49349400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:49335000-49349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:49335200-49349600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:49335400-49349000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:49335400-49349400	Weak transcription	Liver	Liver
16	chr12:49335400-49349800	Weak transcription	Spleen	Spleen
17	chr12:49337600-49349200	Weak transcription	Brain Substantia Nigra	brain
18	chr12:49339200-49348600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:49340000-49348400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:49340000-49349000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49340000-49349200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:49340600-49349400	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:49340800-49348400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:49340800-49349200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:49340800-49349800	Weak transcription	Right Ventricle	heart
26	chr12:49341000-49349000	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:49341400-49349400	Weak transcription	Colonic Mucosa	Colon
28	chr12:49341800-49348800	Strong transcription	Fetal Stomach	stomach
29	chr12:49342000-49348200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:49342400-49348400	Strong transcription	Hela-S3	cervix
31	chr12:49342600-49348000	Strong transcription	Fetal Thymus	thymus
32	chr12:49342800-49348000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:49342800-49348800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:49342800-49349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:49343400-49348000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:49343400-49348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:49344600-49349400	Strong transcription	HSMM	muscle
38	chr12:49344800-49349000	Strong transcription	A549	lung
39	chr12:49345000-49348600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:49345200-49348600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:49345600-49348200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:49345600-49349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:49345800-49348000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:49345800-49348000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:49345800-49348000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:49345800-49348200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr12:49345800-49348200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:49345800-49348400	Strong transcription	NHEK	skin
49	chr12:49345800-49349200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:49346000-49348200	Strong transcription	Rectal Mucosa Donor 29	rectum

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