Variant report

Variant	rs12702633
Chromosome Location	chr7:7704100-7704101
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7679863..7681686-chr7:7702542..7704997,4	K562	blood:
2	chr7:7702478..7704915-chr7:7709957..7711916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219545	Chromatin interaction
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10251718	1.00[JPT][hapmap]
rs12702629	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702632	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13225575	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13227585	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227675	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227682	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229887	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239455	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs13242410	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13247134	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17169196	1.00[JPT][hapmap]
rs17524233	1.00[JPT][hapmap]
rs17545831	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545935	1.00[CEU][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17547731	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2024374	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28915992	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28916005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28916269	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34302387	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34674816	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34820918	1.00[ASN][1000 genomes]
rs34972393	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35202374	1.00[ASN][1000 genomes]
rs35278933	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36130255	1.00[ASN][1000 genomes]
rs59693264	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434910	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463702	1.00[JPT][hapmap]
rs6962939	1.00[JPT][hapmap]
rs6964593	1.00[JPT][hapmap]
rs6974820	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980052	1.00[JPT][hapmap]
rs7789164	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7793870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796049	0.94[CEU][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv887484	chr7:7692483-7769363	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12702633	CYTH3	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7681600-7710200	Weak transcription	Aorta	Aorta
2	chr7:7682000-7713800	Weak transcription	Left Ventricle	heart
3	chr7:7682200-7711600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr7:7687800-7717400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:7690600-7713800	Weak transcription	Fetal Intestine Large	intestine
6	chr7:7691800-7717600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:7692400-7717600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:7693000-7719200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:7693400-7714800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:7694800-7718400	Weak transcription	Ovary	ovary
11	chr7:7696600-7715400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:7699200-7710000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:7699800-7715400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:7701400-7705800	Weak transcription	Gastric	stomach
15	chr7:7701400-7713600	Weak transcription	Thymus	Thymus
16	chr7:7702000-7717000	Weak transcription	Fetal Stomach	stomach
17	chr7:7702000-7717400	Weak transcription	Fetal Intestine Small	intestine
18	chr7:7702200-7715000	Weak transcription	Lung	lung
19	chr7:7702400-7715000	Weak transcription	Adipose Nuclei	Adipose
20	chr7:7702400-7715400	Weak transcription	Pancreas	Pancrea
21	chr7:7702400-7715800	Weak transcription	Spleen	Spleen
22	chr7:7702600-7711800	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:7702800-7704400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:7702800-7704400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr7:7703200-7704400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr7:7703400-7707000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:7703400-7726800	Weak transcription	Brain Germinal Matrix	brain
28	chr7:7703600-7704200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:7703600-7704400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr7:7703600-7704400	Enhancers	HUVEC	blood vessel
31	chr7:7703800-7704400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:7703800-7704400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:7703800-7704400	Enhancers	Stomach Mucosa	stomach
34	chr7:7703800-7705200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr7:7704000-7704200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr7:7704000-7704200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:7704000-7704200	Enhancers	Fetal Kidney	kidney
38	chr7:7704000-7704200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr7:7704000-7704400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:7704000-7704400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:7704000-7704400	Enhancers	Fetal Lung	lung
42	chr7:7704000-7705400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:7704000-7709800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:7704000-7710600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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