Variant report

Variant	rs3173669
Chromosome Location	chr7:50519326-50519327
allele	C/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	MXI1	chr7:50517107-50519658	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50518383..50520516-chr7:50572098..50575046,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FIGNL1-1	chr7:50518506-50521012	ENSG00000248258
2	lnc-FIGNL1-1	chr7:50518449-50521151	XLOC_006441

Variant related genes	Relation type
FIGNL1	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10499693	0.92[EUR][1000 genomes]
rs11575293	0.92[EUR][1000 genomes]
rs11575302	0.92[EUR][1000 genomes]
rs11575340	0.92[EUR][1000 genomes]
rs11575343	0.92[EUR][1000 genomes]
rs11575360	0.92[EUR][1000 genomes]
rs11575381	0.92[EUR][1000 genomes]
rs11575385	0.92[EUR][1000 genomes]
rs11575407	0.92[EUR][1000 genomes]
rs11575447	0.92[EUR][1000 genomes]
rs11575493	0.92[EUR][1000 genomes]
rs11575494	0.92[EUR][1000 genomes]
rs11575501	0.92[EUR][1000 genomes]
rs11575502	0.92[EUR][1000 genomes]
rs11575503	0.92[EUR][1000 genomes]
rs11575504	0.92[EUR][1000 genomes]
rs11575505	0.92[EUR][1000 genomes]
rs11575507	0.92[EUR][1000 genomes]
rs11575508	0.92[EUR][1000 genomes]
rs11575510	0.92[EUR][1000 genomes]
rs11575511	0.92[EUR][1000 genomes]
rs11575512	0.92[EUR][1000 genomes]
rs11575514	0.92[EUR][1000 genomes]
rs11575518	0.92[EUR][1000 genomes]
rs11575519	0.92[EUR][1000 genomes]
rs11575522	0.92[EUR][1000 genomes]
rs11575523	0.92[EUR][1000 genomes]
rs11575527	0.92[EUR][1000 genomes]
rs11575537	0.92[EUR][1000 genomes]
rs11575540	0.92[EUR][1000 genomes]
rs11575542	0.92[EUR][1000 genomes]
rs11575543	0.92[EUR][1000 genomes]
rs11575546	0.92[EUR][1000 genomes]
rs11575547	0.92[EUR][1000 genomes]
rs11575549	0.92[EUR][1000 genomes]
rs11978797	0.85[EUR][1000 genomes]
rs11981575	0.92[EUR][1000 genomes]
rs11982708	0.92[EUR][1000 genomes]
rs11982772	0.92[EUR][1000 genomes]
rs11982776	0.85[EUR][1000 genomes]
rs11983581	0.92[EUR][1000 genomes]
rs11983757	0.92[EUR][1000 genomes]
rs12112308	0.92[EUR][1000 genomes]
rs12113897	0.92[EUR][1000 genomes]
rs2329370	0.92[EUR][1000 genomes]
rs55869201	0.92[EUR][1000 genomes]
rs55992615	0.92[EUR][1000 genomes]
rs56030652	0.92[EUR][1000 genomes]
rs56056130	0.86[AFR][1000 genomes]
rs57167849	1.00[EUR][1000 genomes]
rs57835901	0.92[EUR][1000 genomes]
rs59150746	0.92[EUR][1000 genomes]
rs59828622	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6956737	0.92[EUR][1000 genomes]
rs6975312	0.92[EUR][1000 genomes]
rs6978556	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695512	0.92[EUR][1000 genomes]
rs73695638	0.92[EUR][1000 genomes]
rs73695639	1.00[EUR][1000 genomes]
rs73695640	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73695641	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73695643	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73695661	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73695664	1.00[EUR][1000 genomes]
rs73695666	1.00[EUR][1000 genomes]
rs73695667	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695668	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695669	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695670	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695671	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695672	1.00[EUR][1000 genomes]
rs73695673	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695681	0.92[EUR][1000 genomes]
rs73695682	0.92[EUR][1000 genomes]
rs73695683	0.92[EUR][1000 genomes]
rs73695684	0.92[EUR][1000 genomes]
rs73695700	0.92[EUR][1000 genomes]
rs73695701	0.92[EUR][1000 genomes]
rs73695702	0.92[EUR][1000 genomes]
rs73697528	0.92[EUR][1000 genomes]
rs73697574	0.92[EUR][1000 genomes]
rs930707	0.92[EUR][1000 genomes]
rs9942578	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50518400-50519400	Flanking Active TSS	Dnd41	blood
2	chr7:50518600-50519400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:50518800-50519400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr7:50518800-50519400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr7:50518800-50519400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:50518800-50519400	Enhancers	Fetal Muscle Leg	muscle
7	chr7:50518800-50519400	Enhancers	Right Atrium	heart
8	chr7:50518800-50519400	Enhancers	Small Intestine	intestine
9	chr7:50518800-50521600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:50518800-50522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:50518800-50535400	Weak transcription	Pancreas	Pancrea
12	chr7:50518800-50535600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:50518800-50535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:50518800-50535600	Weak transcription	HepG2	liver
15	chr7:50519000-50519400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:50519000-50519400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr7:50519000-50519400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr7:50519000-50519400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:50519000-50519400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr7:50519000-50523400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:50519000-50523400	Weak transcription	Liver	Liver
22	chr7:50519000-50523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:50519000-50523800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:50519000-50523800	Weak transcription	Fetal Intestine Small	intestine
25	chr7:50519000-50524400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:50519000-50529400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:50519200-50523400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:50519200-50524000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:50519200-50524000	Weak transcription	Fetal Intestine Large	intestine

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