Variant report

Variant	rs11165062
Chromosome Location	chr1:94477634-94477635
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	MAX	chr1:94477458-94478044	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr1:94477332-94477905	H1-hESC	embryonic stem cell:	n/a	chr1:94477423-94477435
3	E2F6	chr1:94477037-94479451	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF263	chr1:94477470-94477898	HEK293-T-REx	kidney:	n/a	chr1:94477719-94477740 chr1:94477687-94477708
5	BHLHE40	chr1:94477578-94477941	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ABCA4	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10874828	0.90[JPT][hapmap]
rs10874829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11165063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110808	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17391612	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801574	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs2065711	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs2065712	0.84[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs2275029	0.87[CHD][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs2275031	0.87[CHD][hapmap];0.89[LWK][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs2275032	0.84[AFR][1000 genomes]
rs2893264	0.84[AFR][1000 genomes]
rs3789379	0.84[AFR][1000 genomes]
rs3789382	0.84[AFR][1000 genomes]
rs3789383	0.84[AFR][1000 genomes]
rs3789384	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs3789385	0.84[AFR][1000 genomes]
rs3789386	0.84[AFR][1000 genomes]
rs3789391	0.82[JPT][hapmap]
rs4147856	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs4147857	0.87[CHD][hapmap];0.87[LWK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs4147859	0.97[ASN][1000 genomes]
rs4147861	0.97[ASN][1000 genomes]
rs4147862	0.87[CHD][hapmap];0.86[YRI][hapmap]
rs4147863	0.87[CHD][hapmap]
rs4147866	0.86[ASN][1000 genomes]
rs55691342	0.85[ASN][1000 genomes]
rs55694362	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56166161	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61782237	0.82[AFR][1000 genomes]
rs7531001	0.91[YRI][hapmap];0.84[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516137	chr1:94404238-94504545	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11165062	C1orf146	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94471200-94480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:94475400-94485600	Weak transcription	NH-A	brain
3	chr1:94475600-94478200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:94476400-94479000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94476400-94479200	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:94476400-94479400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:94476400-94480000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:94476600-94479400	Enhancers	Placenta	Placenta
9	chr1:94476600-94479600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:94476800-94478600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:94476800-94479200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:94476800-94480400	Enhancers	Fetal Intestine Large	intestine
13	chr1:94477000-94478600	Enhancers	Ovary	ovary
14	chr1:94477000-94479000	Enhancers	Right Atrium	heart
15	chr1:94477000-94479400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr1:94477000-94479800	Enhancers	Fetal Intestine Small	intestine
17	chr1:94477000-94481600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:94477200-94478000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:94477200-94478200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr1:94477200-94478600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr1:94477200-94479200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:94477200-94479200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:94477200-94480400	Weak transcription	HMEC	breast
24	chr1:94477400-94478400	Enhancers	Osteobl	bone
25	chr1:94477400-94478600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:94477400-94478600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:94477400-94479800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr1:94477400-94480000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:94477400-94480200	Enhancers	Brain Germinal Matrix	brain
30	chr1:94477600-94477800	Enhancers	Spleen	Spleen
31	chr1:94477600-94477800	Enhancers	HSMM	muscle
32	chr1:94477600-94478200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:94477600-94478600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:94477600-94478600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr1:94477600-94478600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
36	chr1:94477600-94478800	Enhancers	Fetal Stomach	stomach
37	chr1:94477600-94479200	Enhancers	Duodenum Mucosa	Duodenum
38	chr1:94477600-94479200	Enhancers	HepG2	liver
39	chr1:94477600-94479400	Enhancers	H9 Cell Line	embryonic stem cell
40	chr1:94477600-94479400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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