Variant report

Variant	rs1716835
Chromosome Location	chr3:120153464-120153465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120145331..120148802-chr3:120153199..120156349,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1123897	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1123898	0.97[ASN][1000 genomes]
rs1147706	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1147710	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1147720	0.88[CHB][hapmap]
rs1259311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1259318	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1259329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259333	0.85[JPT][hapmap]
rs1259334	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1259335	0.83[JPT][hapmap]
rs1259336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1259337	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259338	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1259339	0.94[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1259471	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259472	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259473	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1267675	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520881	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716837	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733298	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733301	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733303	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733304	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733307	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733319	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252084	0.94[CHB][hapmap]
rs2700263	0.87[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5000757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs874477	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs874478	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874480	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9631455	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1716835	FSTL1	cis	parietal	SCAN
rs1716835	FSTL1	cis	cerebellum	SCAN
rs1716835	NR1I2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:120138200-120154200	Weak transcription	HMEC	breast
4	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:120138200-120169200	Weak transcription	Gastric	stomach
8	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
9	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
10	chr3:120142000-120153600	Genic enhancers	NHLF	lung
11	chr3:120142400-120153600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:120143600-120154200	Genic enhancers	NH-A	brain
13	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:120145400-120157600	Weak transcription	Fetal Brain Female	brain
15	chr3:120145600-120153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
17	chr3:120146800-120157800	Weak transcription	Fetal Brain Male	brain
18	chr3:120147000-120154400	Genic enhancers	HSMMtube	muscle
19	chr3:120147200-120154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:120147600-120154000	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr3:120147600-120154200	Weak transcription	Fetal Intestine Small	intestine
22	chr3:120148000-120153600	Enhancers	Fetal Heart	heart
23	chr3:120148000-120161000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:120149000-120161200	Genic enhancers	NHDF-Ad	bronchial
25	chr3:120149200-120154200	Weak transcription	Small Intestine	intestine
26	chr3:120149200-120155400	Weak transcription	Brain Anterior Caudate	brain
27	chr3:120149200-120156600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:120149400-120155600	Enhancers	Colon Smooth Muscle	Colon
29	chr3:120149400-120157200	Weak transcription	Colonic Mucosa	Colon
30	chr3:120149800-120154000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:120150400-120154200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:120150400-120157400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:120150600-120153600	Enhancers	Right Atrium	heart
34	chr3:120151200-120155400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:120151400-120154200	Weak transcription	Brain Angular Gyrus	brain
36	chr3:120151400-120154200	Weak transcription	Stomach Mucosa	stomach
37	chr3:120151800-120154000	Weak transcription	A549	lung
38	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:120152000-120153800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:120152000-120154200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:120152000-120154200	Genic enhancers	Osteobl	bone
42	chr3:120152000-120155200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:120152000-120158400	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:120152200-120154200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:120152200-120154600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:120152200-120154600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:120152200-120156400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:120152200-120157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:120152400-120154400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:120152400-120154400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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