Variant report

Variant	rs703823
Chromosome Location	chr12:56601237-56601238
allele	C/T
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56600093..56601629-chr12:56651742..56654123,2	MCF-7	breast:
2	chr12:56518676..56520949-chr12:56599005..56601589,2	MCF-7	breast:
3	chr12:56600189..56603854-chr12:56613542..56616774,5	MCF-7	breast:
4	chr12:56598444..56603105-chr12:56614822..56617186,4	K562	blood:
5	chr12:56544774..56546297-chr12:56600523..56602218,2	K562	blood:
6	chr12:56582384..56585175-chr12:56598844..56602261,4	MCF-7	breast:
7	chr12:56319864..56322384-chr12:56600081..56602292,2	MCF-7	breast:
8	chr12:56508809..56510764-chr12:56599083..56602817,4	K562	blood:
9	chr12:56596803..56602914-chr12:56614556..56619492,8	MCF-7	breast:
10	chr12:56554308..56556384-chr12:56600666..56602668,2	K562	blood:
11	chr12:56585299..56590294-chr12:56596188..56601714,8	K562	blood:
12	chr12:56599172..56601403-chr12:56623221..56625855,2	K562	blood:
13	chr12:56510383..56513914-chr12:56599781..56601748,3	MCF-7	breast:
14	chr12:56596235..56598183-chr12:56598582..56601452,2	MCF-7	breast:
15	chr12:56599947..56601470-chr12:56605458..56607820,2	K562	blood:
16	chr12:56598742..56603625-chr12:56603929..56607820,7	K562	blood:
17	chr12:56596901..56601818-chr12:56613329..56617125,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258199	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000266023	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139540	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10747763	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10876878	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171753	1.00[TSI][hapmap]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11171777	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171823	1.00[TSI][hapmap]
rs11834728	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12306670	1.00[TSI][hapmap]
rs12309480	1.00[EUR][1000 genomes]
rs12311878	1.00[TSI][hapmap]
rs12320265	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274502	1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689518	1.00[CHD][hapmap]
rs17118333	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271188	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap]
rs2277340	1.00[CHD][hapmap]
rs2463365	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629451	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2629453	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695783	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28676339	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930787	0.89[AMR][1000 genomes]
rs2930788	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809130	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759218	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs58009483	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59420211	1.00[EUR][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7136420	1.00[TSI][hapmap]
rs7311008	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772925	1.00[TSI][hapmap]
rs772926	1.00[TSI][hapmap]
rs773654	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773655	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs773658	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773659	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773663	1.00[TSI][hapmap]
rs7956599	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7956926	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7962107	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[ASN][1000 genomes]
rs7975486	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs703823	HLA-DPB1	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56592600-56613600	Weak transcription	Right Atrium	heart
3	chr12:56596400-56603800	Weak transcription	Stomach Mucosa	stomach
4	chr12:56596600-56604000	Weak transcription	Small Intestine	intestine
5	chr12:56597800-56602200	Strong transcription	HSMM	muscle
6	chr12:56597800-56610600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:56597800-56610600	Strong transcription	Fetal Lung	lung
8	chr12:56597800-56611600	Strong transcription	Primary T cells from cord blood	blood
9	chr12:56597800-56611600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:56597800-56611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:56597800-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:56597800-56611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:56597800-56611800	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:56597800-56611800	Strong transcription	Fetal Thymus	thymus
15	chr12:56597800-56612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:56598000-56602000	Strong transcription	Fetal Brain Male	brain
17	chr12:56598000-56602200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:56598000-56602200	Strong transcription	Brain Angular Gyrus	brain
19	chr12:56598000-56602200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr12:56598000-56602200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:56598000-56602200	Strong transcription	GM12878-XiMat	blood
22	chr12:56598000-56602200	Strong transcription	NHEK	skin
23	chr12:56598000-56602600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:56598000-56606400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:56598000-56610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:56598000-56610600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:56598000-56610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:56598000-56610600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:56598000-56610600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:56598000-56610600	Strong transcription	Brain Hippocampus Middle	brain
31	chr12:56598000-56610600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr12:56598000-56610600	Strong transcription	Spleen	Spleen
33	chr12:56598000-56611000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:56598000-56611000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr12:56598000-56611600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:56598000-56611600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:56598000-56611600	Strong transcription	Fetal Brain Female	brain
38	chr12:56598000-56611600	Strong transcription	Fetal Intestine Large	intestine
39	chr12:56598000-56611600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:56598000-56611800	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr12:56598000-56613600	Strong transcription	Fetal Stomach	stomach
42	chr12:56598200-56602200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:56598200-56602200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:56598200-56602200	Strong transcription	Brain Substantia Nigra	brain
45	chr12:56598200-56602200	Strong transcription	A549	lung
46	chr12:56598200-56602200	Strong transcription	Dnd41	blood
47	chr12:56598200-56602600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr12:56598200-56603800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:56598200-56609000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:56598200-56609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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