Variant report

Variant	rs12368653
Chromosome Location	chr12:58133256-58133257
allele	A/G
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	RFX5	chr12:58132334-58133513	SK-N-SH	brain:	n/a	chr12:58133399-58133413 chr12:58133395-58133412 chr12:58133396-58133411 chr12:58133401-58133410 chr12:58133396-58133411 chr12:58133396-58133411
2	SP1	chr12:58132494-58133273	A549	lung:	n/a	chr12:58133082-58133095 chr12:58132651-58132660 chr12:58132650-58132662 chr12:58132650-58132662 chr12:58132652-58132661

No.	Distal block	Cell Line	Cell type
1	chr12:57914271..57916098-chr12:58131440..58134732,4	K562	blood:
2	chr12:57916381..57918711-chr12:58131475..58134282,2	MCF-7	breast:
3	chr12:57911286..57913384-chr12:58133067..58135116,2	K562	blood:
4	chr12:58133058..58135797-chr12:58239105..58241667,3	MCF-7	breast:
5	chr12:57909973..57915898-chr12:58127755..58134567,15	K562	blood:

Variant related genes	Relation type
AGAP2	TF binding region
TSPAN31	TF binding region
ENSG00000175215	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10877020	0.89[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs12371356	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17852479	0.89[AMR][1000 genomes]
rs2270777	0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2277324	0.81[MEX][hapmap]
rs2277326	0.82[GIH][hapmap]
rs2307097	0.82[GIH][hapmap]
rs3816896	0.81[EUR][1000 genomes]
rs7966795	0.86[MEX][hapmap]
rs923828	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers 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	39 gene(s)	inside rSNPs	diseases
9	esv3363572	chr12:58129335-58133633	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv826385	chr12:58129908-58133427	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv3408774	chr12:58130710-58133658	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	esv3429081	chr12:58131185-58133683	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
14	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12368653	KIAA0748	cis	cerebellum	SCAN
rs12368653	XRCC6BP1	cis	brain	seeQTL
rs12368653	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs12368653	GPR84	cis	cerebellum	SCAN
rs12368653	XRCC6BP1	cis	Whole Blood	GTEx
rs12368653	XRCC6BP1	cis	Artery Tibial	GTEx
rs12368653	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12368653	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs12368653	FAM119B	cis	lymphoblastoid	seeQTL
rs12368653	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs12368653	TENC1	cis	cerebellum	SCAN
rs12368653	XRCC6BP1	cis	multi-tissue	Pritchard
rs12368653	OR6C4	cis	cerebellum	SCAN
rs12368653	FAM119B	cis	parietal	SCAN
rs12368653	DKFZP586D0919	cis	multi-tissue	Pritchard
rs12368653	FAM119B	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58127800-58133600	Weak transcription	GM12878-XiMat	blood
2	chr12:58130200-58134200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:58131200-58133600	Active TSS	Brain Angular Gyrus	brain
4	chr12:58131200-58134400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:58131200-58138000	Weak transcription	K562	blood
6	chr12:58131600-58133600	Bivalent/Poised TSS	Left Ventricle	heart
7	chr12:58131600-58134600	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:58131800-58138000	Weak transcription	Lung	lung
9	chr12:58132000-58134800	Weak transcription	Spleen	Spleen
10	chr12:58132200-58133400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
11	chr12:58132200-58138800	Weak transcription	Gastric	stomach
12	chr12:58132400-58133600	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr12:58132400-58133600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:58132400-58133800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:58132400-58134200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:58132400-58134400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:58132600-58133400	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr12:58132600-58133600	Enhancers	Primary B cells from cord blood	blood
19	chr12:58132600-58133600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:58132600-58133600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:58132600-58134200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:58132600-58134200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr12:58132800-58133400	Bivalent Enhancer	Adipose Nuclei	Adipose
24	chr12:58132800-58133400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
25	chr12:58132800-58133400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr12:58132800-58133600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:58132800-58133600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:58132800-58133600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr12:58132800-58133800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:58132800-58133800	Bivalent Enhancer	Fetal Brain Male	brain
31	chr12:58132800-58133800	Genic enhancers	Thymus	Thymus
32	chr12:58132800-58133800	Genic enhancers	Dnd41	blood
33	chr12:58132800-58134000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
34	chr12:58132800-58134000	Bivalent Enhancer	Fetal Stomach	stomach
35	chr12:58132800-58134600	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr12:58133000-58133400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr12:58133000-58133400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
38	chr12:58133000-58133400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
39	chr12:58133000-58133600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:58133000-58133600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr12:58133000-58133600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:58133000-58133600	Genic enhancers	Fetal Thymus	thymus
43	chr12:58133000-58133800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:58133000-58133800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:58133000-58134000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
46	chr12:58133000-58134000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:58133000-58134000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr12:58133000-58134200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:58133000-58134400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:58133200-58133400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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