Variant report

Variant	rs11103902
Chromosome Location	chr12:86650173-86650174
allele	C/T
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	SIN3AK20	chr12:86649946-86650309	PFSK-1	brain:	n/a	n/a
2	TAF1	chr12:86649921-86650217	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:86649868-86650387	H1-neurons	neurons:	n/a	n/a
4	KAP1	chr12:86649928-86650379	U2OS	brain:	n/a	n/a
5	FOXA1	chr12:86649974-86650278	T-47D	breast:	n/a	n/a
6	POLR2A	chr12:86649901-86650443	H1-neurons	neurons:	n/a	n/a
7	FOXP2	chr12:86649982-86650311	PFSK-1	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGAT4C-1	chr12:86650017-86650192	NONHSAT029760

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10160933	1.00[YRI][hapmap]
rs11103901	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11103905	1.00[AFR][1000 genomes]
rs11103906	1.00[AFR][1000 genomes]
rs11103907	1.00[AFR][1000 genomes]
rs11103910	1.00[YRI][hapmap]
rs11103922	0.87[YRI][hapmap]
rs11103937	1.00[YRI][hapmap]
rs11103956	1.00[YRI][hapmap]
rs11103959	0.88[YRI][hapmap]
rs12296316	0.88[YRI][hapmap]
rs12298208	1.00[AFR][1000 genomes]
rs12298422	1.00[AFR][1000 genomes]
rs12299772	1.00[AFR][1000 genomes]
rs12299950	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12300410	0.84[AFR][1000 genomes]
rs12303146	0.88[AFR][1000 genomes]
rs12304625	1.00[YRI][hapmap]
rs12305480	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12306070	1.00[YRI][hapmap]
rs12306455	1.00[AFR][1000 genomes]
rs12306583	0.94[AFR][1000 genomes]
rs12306726	1.00[YRI][hapmap]
rs12308711	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12309297	1.00[AFR][1000 genomes]
rs12311208	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12311647	1.00[YRI][hapmap]
rs12315031	1.00[AFR][1000 genomes]
rs12316205	0.88[AFR][1000 genomes]
rs12316480	1.00[YRI][hapmap]
rs12318124	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12318366	1.00[YRI][hapmap]
rs12318727	0.88[AFR][1000 genomes]
rs12318998	1.00[YRI][hapmap]
rs12319070	0.88[YRI][hapmap]
rs12321412	1.00[YRI][hapmap]
rs12321784	0.87[YRI][hapmap]
rs4842468	1.00[YRI][hapmap]
rs9971936	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86644200-86655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:86648200-86650600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:86648400-86650400	Active TSS	Brain Anterior Caudate	brain
4	chr12:86648600-86650200	Active TSS	Fetal Heart	heart
5	chr12:86648600-86650400	Active TSS	Right Atrium	heart
6	chr12:86649000-86651000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:86649600-86650400	Active TSS	Brain Cingulate Gyrus	brain
8	chr12:86649600-86650400	Active TSS	Right Ventricle	heart
9	chr12:86649800-86650200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr12:86649800-86650200	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr12:86649800-86650200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:86649800-86650400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:86649800-86651000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr12:86649800-86651400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:86650000-86650200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:86650000-86650200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:86650000-86650200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:86650000-86650200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:86650000-86650200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:86650000-86650200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:86650000-86650200	Enhancers	Left Ventricle	heart
22	chr12:86650000-86650400	Active TSS	Brain Angular Gyrus	brain
23	chr12:86650000-86650400	Active TSS	Brain Hippocampus Middle	brain
24	chr12:86650000-86650400	Enhancers	Brain Substantia Nigra	brain
25	chr12:86650000-86650400	Enhancers	Fetal Lung	lung
26	chr12:86650000-86651200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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