Variant report

Variant	rs1412335
Chromosome Location	chr1:168658880-168658881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168658040..168660028-chr1:169075019..169076893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489358	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489359	0.81[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10918958	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588432	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588434	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11590795	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11799741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094644	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726636	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12727749	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745063	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12748015	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749426	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749876	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337747	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337748	0.85[EUR][1000 genomes]
rs1412334	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1412336	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415678	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415680	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16861287	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502304	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502351	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502574	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17561671	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223911	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2419126	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2419128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34099957	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35492795	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4437856	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58620990	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688592	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs726055	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416358	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001684	chr1:168636622-168663398	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv525556	chr1:168653857-168662352	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv819134	chr1:168658217-168659214	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1412335	SELL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168655200-168659600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr1:168656200-168660800	Enhancers	Colon Smooth Muscle	Colon
3	chr1:168657000-168661000	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:168657200-168659400	Enhancers	Stomach Mucosa	stomach
5	chr1:168657200-168660600	Enhancers	Fetal Heart	heart
6	chr1:168657400-168659400	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr1:168657600-168659600	Enhancers	Ovary	ovary
8	chr1:168657800-168660000	Enhancers	A549	lung
9	chr1:168657800-168660400	Enhancers	Fetal Intestine Small	intestine
10	chr1:168658000-168659000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:168658000-168660000	Enhancers	Fetal Intestine Large	intestine
12	chr1:168658000-168660000	Enhancers	Fetal Stomach	stomach
13	chr1:168658000-168660600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:168658000-168662000	Enhancers	Pancreas	Pancrea
15	chr1:168658200-168662000	Weak transcription	Fetal Kidney	kidney
16	chr1:168658200-168662400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:168658200-168662800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:168658200-168663200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:168658400-168661000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:168658600-168659200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:168658600-168659400	Enhancers	Small Intestine	intestine
22	chr1:168658600-168659600	Enhancers	Gastric	stomach
23	chr1:168658600-168659600	Enhancers	Right Ventricle	heart
24	chr1:168658800-168659400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:168658800-168659600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:168658800-168659600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:168658800-168659600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:168658800-168660000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:168658800-168660000	Flanking Active TSS	HepG2	liver

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