Variant report

Variant	rs907868
Chromosome Location	chr2:20371167-20371168
allele	A/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	NR3C1	chr2:20371025-20371330	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20101674..20103205-chr2:20369213..20371363,2	MCF-7	breast:
2	chr2:20369269..20371931-chr2:20376136..20379582,4	MCF-7	breast:

Variant related genes	Relation type
RNU6-961P	TF binding region
RN7SL140P	TF binding region
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1107850	0.88[CEU][hapmap];0.83[CHB][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1107851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1107852	0.84[JPT][hapmap]
rs11096641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11693335	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11895352	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11899121	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009332	0.85[CHB][hapmap]
rs13010903	0.85[CHB][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs1473886	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2090032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2090034	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6728072	0.85[CHB][hapmap]
rs7577335	0.85[CHB][hapmap]
rs870526	0.81[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs870527	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907867	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs907868	SDC1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20362400-20371400	Weak transcription	Right Atrium	heart
2	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:20364400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:20364800-20372200	Enhancers	NHEK	skin
5	chr2:20366000-20371200	Weak transcription	Fetal Lung	lung
6	chr2:20366400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:20366600-20371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:20366800-20372600	Enhancers	Placenta	Placenta
9	chr2:20367200-20376600	Weak transcription	Stomach Mucosa	stomach
10	chr2:20367400-20372200	Weak transcription	GM12878-XiMat	blood
11	chr2:20367600-20371200	Weak transcription	Pancreas	Pancrea
12	chr2:20367600-20371200	Weak transcription	HMEC	breast
13	chr2:20367800-20383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:20369000-20374400	Enhancers	Esophagus	oesophagus
15	chr2:20369600-20371400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:20369600-20371800	Enhancers	Fetal Intestine Large	intestine
17	chr2:20369600-20377800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:20369800-20371800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:20369800-20371800	Enhancers	Fetal Intestine Small	intestine
20	chr2:20369800-20374200	Enhancers	Liver	Liver
21	chr2:20370000-20371200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:20370000-20373200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:20370200-20371200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:20370200-20371400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:20370200-20371400	Enhancers	HepG2	liver
26	chr2:20370200-20372000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:20370200-20372000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:20370200-20379800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20370400-20372200	Enhancers	Fetal Kidney	kidney
30	chr2:20370600-20372000	Weak transcription	Brain Germinal Matrix	brain
31	chr2:20370800-20371600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:20370800-20372000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:20370800-20372400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:20370800-20372400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:20371000-20371400	Weak transcription	Lung	lung
36	chr2:20371000-20371600	Enhancers	Duodenum Mucosa	Duodenum
37	chr2:20371000-20372600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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