Variant report

Variant	rs10783828
Chromosome Location	chr12:57861484-57861485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57855142..57857395-chr12:57860962..57863336,2	K562	blood:
2	chr12:57855507..57859311-chr12:57860287..57863469,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111087	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10783826	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783827	0.95[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10876986	0.81[ASN][1000 genomes]
rs10876987	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11544238	0.81[JPT][hapmap]
rs2228224	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2228225	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2228226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277317	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277318	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292657	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782125	0.81[ASN][1000 genomes]
rs3782126	0.87[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3817474	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817475	0.81[ASN][1000 genomes]
rs3825077	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4760148	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs4760259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309467	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a
14	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
15	nsv559035	chr12:57860972-57870648	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10783828	DKFZP586D0919	cis	multi-tissue	Pritchard
rs10783828	ATF7	cis	cerebellum	SCAN
rs10783828	XRCC6BP1	cis	multi-tissue	Pritchard
rs10783828	FAM119B	cis	cerebellum	SCAN
rs10783828	OR6C4	cis	parietal	SCAN
rs10783828	CDK4	cis	cerebellum	SCAN
rs10783828	RDH5	cis	cerebellum	SCAN
rs10783828	KIAA0748	cis	cerebellum	SCAN
rs10783828	ITGB7	cis	cerebellum	SCAN
rs10783828	DNAJC14	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57856200-57863200	Weak transcription	Gastric	stomach
2	chr12:57856600-57863200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:57856600-57865800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:57856800-57863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:57856800-57863000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:57856800-57863800	Weak transcription	Fetal Kidney	kidney
7	chr12:57856800-57864400	Weak transcription	Liver	Liver
8	chr12:57856800-57864800	Strong transcription	Fetal Lung	lung
9	chr12:57856800-57865000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:57856800-57865600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:57856800-57866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:57857000-57861800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:57857000-57862800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:57857000-57862800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:57857000-57863000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:57857000-57863000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:57857000-57863000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:57857000-57863000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:57857000-57863000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:57857000-57863200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:57857000-57864200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:57857000-57865800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:57857000-57868400	Weak transcription	Dnd41	blood
24	chr12:57857000-57869400	Weak transcription	Ovary	ovary
25	chr12:57857200-57862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:57857200-57866200	Strong transcription	Fetal Stomach	stomach
27	chr12:57857400-57865800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:57857800-57865400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:57858000-57861800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:57858000-57863000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:57858000-57863000	Strong transcription	Fetal Intestine Small	intestine
32	chr12:57858600-57864400	Weak transcription	Colonic Mucosa	Colon
33	chr12:57859400-57861800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:57859400-57865800	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:57859600-57870800	Weak transcription	A549	lung
36	chr12:57859800-57861600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:57859800-57861600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:57859800-57862800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr12:57859800-57864200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:57860000-57862800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:57860000-57863000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:57860200-57863200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:57860600-57866200	Strong transcription	Primary T cells from cord blood	blood
44	chr12:57860800-57862000	Enhancers	GM12878-XiMat	blood
45	chr12:57861000-57861800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:57861000-57862200	Strong transcription	Thymus	Thymus
47	chr12:57861000-57863000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:57861000-57863800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:57861000-57864000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:57861000-57864000	Strong transcription	Spleen	Spleen

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