Variant report

Variant	rs7315904
Chromosome Location	chr12:835074-835075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:833323..835547-chr12:862208..864227,2	K562	blood:
2	chr12:831910..837502-chr12:858732..864374,10	MCF-7	breast:
3	chr12:751484..754177-chr12:833162..836032,2	MCF-7	breast:
4	chr12:832284..837801-chr12:858821..863136,6	MCF-7	breast:
5	chr12:739580..743706-chr12:833762..836788,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177406	Chromatin interaction
ENSG00000060237	Chromatin interaction
ENSG00000171840	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12305466	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311979	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916725	1.00[ASN][1000 genomes]
rs7138400	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783504	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
9	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
11	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv898567	chr12:547683-863517	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer 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	34 gene(s)	inside rSNPs	diseases
14	nsv491937	chr12:574727-835424	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
15	nsv1049625	chr12:595867-840090	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv541331	chr12:595867-840090	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv556887	chr12:632240-867504	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
18	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
19	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
20	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
21	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
22	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
23	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
24	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv1043718	chr12:786563-855811	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv541339	chr12:786563-855811	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv1046707	chr12:792110-910520	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
28	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
29	esv2754685	chr12:835074-936468	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	esv2753750	chr12:835074-939480	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	esv2753658	chr12:835074-964506	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7315904	C12orf4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:822000-835600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:828600-835200	Weak transcription	Spleen	Spleen
3	chr12:828600-838400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:828800-835200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:828800-835400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:828800-835400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:828800-835600	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:831400-840600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:831600-838000	Enhancers	Primary T cells from cord blood	blood
10	chr12:832000-835200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:832000-835400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:832000-835400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:832000-835600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:832600-837800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:832600-839200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:832600-840400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:832800-836000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:832800-836000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr12:832800-840000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:832800-840200	Enhancers	Fetal Thymus	thymus
21	chr12:833000-840000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:833000-841200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:833200-837600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:833400-836800	Enhancers	Fetal Heart	heart
25	chr12:833400-836800	Enhancers	Fetal Muscle Leg	muscle
26	chr12:833400-837000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:833400-837000	Enhancers	NHEK	skin
28	chr12:833400-838600	Enhancers	HSMM	muscle
29	chr12:833400-839000	Enhancers	Primary hematopoietic stem cells	blood
30	chr12:833800-835200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:834000-835200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:834000-835400	Weak transcription	HMEC	breast
33	chr12:834000-835600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:834000-836000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:834000-836600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:834000-836800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:834000-837400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:834200-836200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:834600-835600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:834600-835600	Weak transcription	Left Ventricle	heart
41	chr12:834600-836600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:834600-838000	Weak transcription	GM12878-XiMat	blood
43	chr12:834800-837600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr12:834800-840400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr12:835000-835800	Enhancers	Right Atrium	heart
46	chr12:835000-836000	Enhancers	Thymus	Thymus
47	chr12:835000-836200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr12:835000-836400	Enhancers	Brain Substantia Nigra	brain
49	chr12:835000-836800	Enhancers	A549	lung
50	chr12:835000-838200	Enhancers	HSMMtube	muscle

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