Variant report

Variant	rs704582
Chromosome Location	chr3:99571926-99571927
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	POLR2A	chr3:99571804-99576711	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:99571886-99571941	ProgFib	skin:	n/a	n/a
3	POLR2A	chr3:99571787-99571938	HepG2	liver:	n/a	n/a
4	JUND	chr3:99571752-99572003	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:99571752-99572142	HepG2	liver:	n/a	n/a
6	GATA1	chr3:99571664-99572236	PBDE	blood:	n/a	chr3:99571947-99571956 chr3:99571920-99571928 chr3:99571944-99571960 chr3:99571942-99571963

No.	Distal block	Cell Line	Cell type
1	chr3:99571584..99573287-chr3:99980510..99983253,2	K562	blood:
2	chr3:99570458..99572667-chr3:99573247..99575806,2	MCF-7	breast:
3	chr3:99566203..99568540-chr3:99570392..99572106,2	MCF-7	breast:
4	chr3:99564230..99568192-chr3:99570896..99574736,4	K562	blood:

Variant related genes	Relation type
FILIP1L	TF binding region
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10049383	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1016914	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1021102	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs1021103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10212525	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs1038294	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10511177	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1087198	0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap]
rs10936005	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs10936008	0.91[JPT][hapmap]
rs1287283	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs13064704	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13317017	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs1489816	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs16841679	0.81[CHB][hapmap]
rs1688766	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[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1688771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688772	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688782	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1718246	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17392948	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.83[MKK][hapmap]
rs2452320	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs2452321	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs28714363	0.81[EUR][1000 genomes]
rs35521705	0.81[EUR][1000 genomes]
rs4075038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244711	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs4244713	0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs4279135	0.81[EUR][1000 genomes]
rs4361315	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap]
rs4479633	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs4571265	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs4928149	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.83[MKK][hapmap];0.81[EUR][1000 genomes]
rs4928232	0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs4928234	0.82[EUR][1000 genomes]
rs629120	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs6440938	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs6765027	0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs6799379	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6807176	0.88[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6809988	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs694429	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs704570	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs704573	0.81[JPT][hapmap]
rs704581	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs704583	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap]
rs7609729	1.00[JPT][hapmap]
rs7610486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs7616988	0.94[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629426	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7636447	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs7638900	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs792834	0.93[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs793440	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793445	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793452	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793453	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793460	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793461	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793462	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs793463	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs793465	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs793466	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs793467	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap]
rs793468	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs793470	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793472	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793474	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793488	0.87[AMR][1000 genomes]
rs793492	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793494	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap]
rs793495	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap]
rs793496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793499	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[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793503	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs796977	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs796978	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs809415	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs812657	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs923470	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs923471	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9810235	0.81[EUR][1000 genomes]
rs9832186	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs9833888	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs9833980	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs9851645	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9852435	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9864437	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs9872871	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs9873709	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9873878	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs9875640	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9878931	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs704582	LRRC37A	trans	brain	seeQTL
rs704582	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL
rs704582	SLC35E1	trans	brain	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
4	chr3:99559000-99578000	Weak transcription	HMEC	breast
5	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:99562200-99578000	Weak transcription	NHEK	skin
7	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
8	chr3:99562800-99580200	Weak transcription	Gastric	stomach
9	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
10	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:99563200-99572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:99563200-99574800	Weak transcription	Psoas Muscle	Psoas
13	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:99563800-99574800	Weak transcription	Pancreas	Pancrea
15	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:99565000-99572000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:99565400-99577600	Weak transcription	Fetal Heart	heart
19	chr3:99565600-99573600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:99565600-99573600	Weak transcription	Fetal Lung	lung
21	chr3:99565600-99574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:99565600-99574800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:99565600-99589400	Weak transcription	K562	blood
25	chr3:99566000-99572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:99566000-99573200	Weak transcription	Liver	Liver
27	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:99567200-99572000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:99567600-99573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:99567600-99576200	Weak transcription	Stomach Mucosa	stomach
31	chr3:99567800-99572800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:99567800-99573400	Strong transcription	HepG2	liver
33	chr3:99567800-99581600	Weak transcription	Spleen	Spleen
34	chr3:99568000-99578600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:99568000-99580000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:99568400-99572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:99568400-99575000	Weak transcription	GM12878-XiMat	blood
38	chr3:99568400-99576000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:99568600-99577600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:99568800-99574800	Weak transcription	NHDF-Ad	bronchial
41	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
42	chr3:99569400-99572200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:99569800-99572800	Weak transcription	HSMMtube	muscle
44	chr3:99569800-99573400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:99569800-99573400	Weak transcription	Fetal Intestine Small	intestine
46	chr3:99569800-99575000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:99569800-99579200	Weak transcription	Right Ventricle	heart
48	chr3:99569800-99579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:99569800-99580200	Weak transcription	Lung	lung
50	chr3:99570000-99572800	Weak transcription	Adipose Nuclei	Adipose

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