Variant report

Variant	rs6690803
Chromosome Location	chr1:227189106-227189107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227189106..227191574-chr1:227196379..227198495,2	K562	blood:
2	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
3	chr1:227176058..227178515-chr1:227186795..227190068,3	MCF-7	breast:
4	chr1:227182754..227185276-chr1:227188097..227190742,3	K562	blood:
5	chr1:227178460..227180582-chr1:227186986..227189766,2	K562	blood:

Variant related genes	Relation type
ENSG00000233706	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1045252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1045285	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1045286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045287	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1045289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916075	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11577007	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11578103	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11578479	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11580229	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11586604	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587443	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588904	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11589344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403236	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12406714	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12409230	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12409428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409755	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12410103	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12593	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1343743	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1343744	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17528667	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17592479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17600627	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17600669	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600725	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1929862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1929863	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1929864	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2104860	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2183836	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297412	0.95[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297415	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2297416	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2297418	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738725	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738729	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3768419	0.81[ASW][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3768421	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768423	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768424	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795445	0.81[ASW][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3795446	0.81[ASW][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3795449	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3795451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795453	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61834001	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61834004	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834005	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834006	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426558	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6426559	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659424	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670924	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6677602	0.92[CEU][hapmap]
rs6684821	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693535	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6699400	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704144	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68087483	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535826	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7541033	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7549465	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7549586	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552783	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9726097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9727512	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6690803	CABC1	cis	parietal	SCAN
rs6690803	ADCK3	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:227175200-227198400	Weak transcription	A549	lung
4	chr1:227175200-227210200	Weak transcription	HMEC	breast
5	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
7	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:227176000-227216400	Weak transcription	NHLF	lung
9	chr1:227176400-227190400	Weak transcription	Osteobl	bone
10	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
12	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
14	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
18	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
19	chr1:227179600-227213800	Weak transcription	NH-A	brain
20	chr1:227180800-227190200	Weak transcription	K562	blood
21	chr1:227181200-227190400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:227181600-227191200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:227182000-227190200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:227182200-227190200	Weak transcription	Ovary	ovary
26	chr1:227182200-227205600	Weak transcription	Fetal Brain Male	brain
27	chr1:227182400-227190800	Weak transcription	NHEK	skin
28	chr1:227182600-227190000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:227182600-227190200	Weak transcription	Gastric	stomach
30	chr1:227182600-227190200	Weak transcription	Right Ventricle	heart
31	chr1:227182600-227191400	Weak transcription	Fetal Kidney	kidney
32	chr1:227182600-227206400	Weak transcription	Brain Germinal Matrix	brain
33	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
34	chr1:227183000-227190200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:227183000-227190400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:227183000-227191000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:227183200-227190200	Weak transcription	Brain Angular Gyrus	brain
38	chr1:227183200-227202600	Weak transcription	Pancreas	Pancrea
39	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
41	chr1:227183600-227204600	Weak transcription	HepG2	liver
42	chr1:227183800-227203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:227184000-227190400	Weak transcription	Fetal Heart	heart
44	chr1:227184000-227191000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:227184000-227203200	Weak transcription	Brain Substantia Nigra	brain
46	chr1:227184000-227204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:227184000-227214600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227184200-227190000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:227184200-227190800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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