Variant report

Variant	rs9877854
Chromosome Location	chr3:119245747-119245748
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119187617..119189310-chr3:119243541..119246268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1060569	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934493	0.85[ASW][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs13080905	0.94[ASN][1000 genomes]
rs1797839	0.91[ASN][1000 genomes]
rs1900742	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919590	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976919	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030816	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814397	0.91[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687860	0.94[ASN][1000 genomes]
rs4688005	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688008	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688014	0.89[ASN][1000 genomes]
rs6414282	0.91[ASN][1000 genomes]
rs6414283	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6438529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438535	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6778945	0.92[ASN][1000 genomes]
rs6794822	0.91[ASN][1000 genomes]
rs6796970	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs727905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73189804	0.83[AFR][1000 genomes]
rs73189805	0.85[AFR][1000 genomes]
rs7430798	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7621259	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628626	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630587	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289129	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9809155	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836326	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850447	0.92[ASN][1000 genomes]
rs9867768	0.88[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9873196	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9877854	FSTL1	cis	cerebellum	SCAN
rs9877854	SRSF2	trans	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
2	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
4	chr3:119237800-119245800	Weak transcription	Small Intestine	intestine
5	chr3:119237800-119246000	Weak transcription	Right Ventricle	heart
6	chr3:119237800-119246400	Weak transcription	Pancreas	Pancrea
7	chr3:119237800-119246600	Weak transcription	Esophagus	oesophagus
8	chr3:119237800-119248000	Weak transcription	Aorta	Aorta
9	chr3:119237800-119251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:119237800-119255800	Weak transcription	Spleen	Spleen
11	chr3:119238000-119248400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:119238200-119245800	Weak transcription	NHEK	skin
13	chr3:119238200-119249000	Weak transcription	NHLF	lung
14	chr3:119238800-119246800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:119239600-119248400	Weak transcription	HSMMtube	muscle
16	chr3:119239600-119253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:119239800-119247400	Weak transcription	Fetal Heart	heart
18	chr3:119239800-119252400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:119240200-119248600	Weak transcription	Fetal Brain Male	brain
20	chr3:119240400-119246000	Weak transcription	Ovary	ovary
21	chr3:119240600-119245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:119240600-119245800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:119240600-119245800	Weak transcription	Psoas Muscle	Psoas
24	chr3:119240600-119246600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:119240600-119246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:119240600-119247400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:119240600-119249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:119242400-119246400	Weak transcription	Gastric	stomach
29	chr3:119242400-119246800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:119243000-119246600	Weak transcription	HepG2	liver
31	chr3:119243000-119247400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:119243000-119248600	Weak transcription	NHDF-Ad	bronchial
33	chr3:119243200-119245800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:119243200-119251400	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:119243400-119248400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:119243600-119246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:119243600-119246000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:119243600-119246000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:119243600-119246600	Weak transcription	Lung	lung
40	chr3:119243600-119246600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:119243600-119246800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:119243600-119247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:119243600-119249400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:119243600-119250800	Weak transcription	Brain Anterior Caudate	brain
45	chr3:119243800-119248800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:119244000-119248200	Weak transcription	HSMM	muscle
47	chr3:119244200-119245800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:119244200-119246800	Weak transcription	Primary T cells from cord blood	blood
49	chr3:119244200-119253400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:119244400-119245800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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