Variant report

Variant	rs3112198
Chromosome Location	chr2:39002142-39002143
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:39002042-39002685	K562	blood:	n/a	n/a
2	BHLHE40	chr2:39002080-39002219	K562	blood:	n/a	n/a
3	ELF1	chr2:39002097-39002388	K562	blood:	n/a	n/a
4	FOSL2	chr2:39002085-39002619	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
2	chr2:38995074..38996747-chr2:39000854..39003003,2	MCF-7	breast:
3	chr2:39000825..39002881-chr2:39004010..39005901,3	MCF-7	breast:
4	chr2:38974922..38979621-chr2:38998984..39003561,8	K562	blood:
5	chr2:39001847..39003662-chr2:39018997..39021441,2	K562	blood:

No data

Variant related genes	Relation type
GEMIN6	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10173118	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10173240	0.86[EUR][1000 genomes]
rs10197412	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865143	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865144	0.86[EUR][1000 genomes]
rs11694383	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11889280	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12465043	0.86[EUR][1000 genomes]
rs12469681	0.94[EUR][1000 genomes]
rs12472454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12473036	0.94[EUR][1000 genomes]
rs12474770	0.87[ASN][1000 genomes]
rs12477252	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12618118	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621103	0.85[ASN][1000 genomes]
rs12991609	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12996194	0.88[EUR][1000 genomes]
rs13011522	0.93[EUR][1000 genomes]
rs13014136	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13024811	0.85[ASN][1000 genomes]
rs13029406	0.89[EUR][1000 genomes]
rs13383541	0.88[EUR][1000 genomes]
rs13411868	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13417196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1530852	0.93[EUR][1000 genomes]
rs1530853	0.92[EUR][1000 genomes]
rs1979142	0.87[EUR][1000 genomes]
rs1979143	0.88[ASN][1000 genomes]
rs2037875	0.84[EUR][1000 genomes]
rs3097713	0.83[ASN][1000 genomes]
rs3099952	0.83[AFR][1000 genomes]
rs3099961	0.96[ASN][1000 genomes]
rs3099965	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3099968	0.91[ASN][1000 genomes]
rs3099971	0.93[ASN][1000 genomes]
rs3099975	0.81[ASN][1000 genomes]
rs3099977	0.81[ASN][1000 genomes]
rs3099980	0.85[ASN][1000 genomes]
rs3099990	0.81[ASN][1000 genomes]
rs3099992	0.81[ASN][1000 genomes]
rs3108666	0.82[ASN][1000 genomes]
rs3112140	0.86[EUR][1000 genomes]
rs3112142	0.85[ASN][1000 genomes]
rs3112143	0.81[ASN][1000 genomes]
rs3112150	0.85[ASN][1000 genomes]
rs3112152	0.82[ASN][1000 genomes]
rs3112156	0.82[ASN][1000 genomes]
rs3112161	0.82[ASN][1000 genomes]
rs3112183	0.88[ASN][1000 genomes]
rs3112184	0.93[ASN][1000 genomes]
rs3112186	0.93[ASN][1000 genomes]
rs3112188	0.93[ASN][1000 genomes]
rs3112189	0.93[ASN][1000 genomes]
rs3112191	0.93[ASN][1000 genomes]
rs3112192	0.93[ASN][1000 genomes]
rs3112194	0.94[ASN][1000 genomes]
rs3112196	0.96[ASN][1000 genomes]
rs3112200	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3112204	0.96[ASN][1000 genomes]
rs3112205	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3112210	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3112216	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3134628	0.88[ASN][1000 genomes]
rs3134629	0.88[ASN][1000 genomes]
rs3134630	0.88[ASN][1000 genomes]
rs3134637	0.91[ASN][1000 genomes]
rs35387882	0.93[ASN][1000 genomes]
rs4602206	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4630748	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4670892	0.87[ASN][1000 genomes]
rs4670897	0.86[EUR][1000 genomes]
rs56393601	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62144837	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6715866	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746818	0.81[ASN][1000 genomes]
rs6753251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7419616	0.93[EUR][1000 genomes]
rs7419838	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs756338	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3112198	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:38999200-39003600	Weak transcription	Placenta	Placenta
4	chr2:38999400-39004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:38999400-39004600	Weak transcription	A549	lung
6	chr2:39000000-39004800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:39001600-39002200	Enhancers	HepG2	liver
8	chr2:39002000-39002600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:39002000-39002600	Enhancers	K562	blood

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