Variant report

Variant	rs6677146
Chromosome Location	chr1:223838950-223838951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223833118..223836523-chr1:223838327..223841763,4	MCF-7	breast:
2	chr1:223834427..223836360-chr1:223837595..223841642,3	MCF-7	breast:
3	chr1:223838928..223839586-chr1:223857876..223858715,2	MCF-7	breast:
4	chr1:223829687..223833751-chr1:223837016..223839699,4	MCF-7	breast:
5	chr1:223837812..223840547-chr1:223845364..223849589,4	K562	blood:
6	chr1:223803243..223805245-chr1:223838331..223840277,2	MCF-7	breast:
7	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction
ENSG00000227002	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495210	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495212	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799570	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1109222	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1125346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408619	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566877	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16842027	0.85[CEU][hapmap]
rs2186009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34089008	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653518	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653523	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653859	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653863	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4653868	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653870	0.82[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653877	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57611697	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60773808	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61825210	0.82[AFR][1000 genomes]
rs61825220	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661481	0.90[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6662068	0.82[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs6671050	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687391	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687688	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691383	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6693911	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6701150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68072917	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72629690	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72629691	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6677146	SUSD4	cis	parietal	SCAN
rs6677146	MRPL14	trans	parietal	SCAN
rs6677146	AIDA	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223830400-223841800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:223833600-223850800	Weak transcription	Colonic Mucosa	Colon
3	chr1:223834200-223840200	Weak transcription	Gastric	stomach
4	chr1:223834200-223841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:223834400-223841600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:223835400-223840200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:223835800-223840200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:223836000-223840200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:223836400-223840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:223836400-223840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:223836600-223840200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:223836600-223840800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:223837000-223839200	Weak transcription	Fetal Brain Male	brain
14	chr1:223837000-223840200	Weak transcription	Esophagus	oesophagus
15	chr1:223837200-223840200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:223837400-223839600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:223837800-223839000	Enhancers	Right Atrium	heart
18	chr1:223837800-223840800	Enhancers	Fetal Lung	lung
19	chr1:223838000-223840800	Enhancers	Psoas Muscle	Psoas
20	chr1:223838200-223841400	Enhancers	Fetal Muscle Leg	muscle
21	chr1:223838200-223842600	Weak transcription	Lung	lung
22	chr1:223838200-223850800	Weak transcription	Fetal Stomach	stomach
23	chr1:223838400-223839200	Enhancers	Colon Smooth Muscle	Colon
24	chr1:223838400-223839400	Genic enhancers	Stomach Mucosa	stomach
25	chr1:223838800-223839600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:223838800-223840000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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