Variant report

Variant	rs7303889
Chromosome Location	chr12:25254975-25254976
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:25253071-25257079	GM12878	blood:	n/a	n/a
2	CTCF	chr12:25254880-25255030	AG10803	skin:	n/a	n/a

Variant related genes	Relation type
LRMP	TF binding region
ENSG00000258449	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10743543	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771172	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842474	0.84[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842479	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842480	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842481	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842482	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842484	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842485	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842513	1.00[CHD][hapmap]
rs11047853	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047863	1.00[CHD][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047864	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313024	0.89[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979522	1.00[CHD][hapmap]
rs2200402	1.00[CHD][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200408	0.82[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220193	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220195	1.00[CHD][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246226	1.00[CHD][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280085	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291763	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4418900	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427639	0.84[EUR][1000 genomes]
rs4460902	0.84[EUR][1000 genomes]
rs4491339	1.00[CHD][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963854	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55746605	1.00[ASN][1000 genomes]
rs57579413	1.00[ASN][1000 genomes]
rs60110571	1.00[ASN][1000 genomes]
rs61391424	1.00[ASN][1000 genomes]
rs6487454	0.81[AFR][1000 genomes]
rs6487455	0.85[AFR][1000 genomes]
rs7132146	1.00[CHD][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133919	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298884	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299464	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488357	0.84[EUR][1000 genomes]
rs7957575	0.80[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959689	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966158	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966255	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976254	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7303889	GUCY1B3	trans	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
5	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
7	chr12:25238600-25265200	Weak transcription	Lung	lung
8	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:25246400-25264000	Weak transcription	Ovary	ovary
11	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
12	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
13	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:25248600-25257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:25248800-25255800	Strong transcription	Thymus	Thymus
18	chr12:25248800-25258000	Strong transcription	Dnd41	blood
19	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:25250600-25256000	Weak transcription	Esophagus	oesophagus
23	chr12:25251400-25255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
25	chr12:25252200-25257000	Weak transcription	Fetal Intestine Large	intestine
26	chr12:25252200-25264000	Weak transcription	Spleen	Spleen
27	chr12:25252400-25260400	Weak transcription	Adipose Nuclei	Adipose
28	chr12:25253200-25255600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:25253200-25262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:25254000-25255400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:25254000-25256000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:25254000-25257000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:25254000-25257400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:25254000-25260200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:25254200-25259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:25254200-25260400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr12:25254200-25263600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:25254200-25263800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:25254200-25263800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:25254400-25260600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:25254600-25256000	Strong transcription	Liver	Liver
42	chr12:25254800-25257400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:25254800-25257600	Strong transcription	GM12878-XiMat	blood

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