Variant report

Variant	rs12535629
Chromosome Location	chr7:100451732-100451733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100448636..100452358-chr7:100462094..100466806,6	K562	blood:
2	chr7:100424369..100426851-chr7:100449777..100451891,3	MCF-7	breast:
3	chr7:100422507..100426422-chr7:100448675..100454510,8	MCF-7	breast:
4	chr7:100450046..100452057-chr7:100463309..100465619,3	MCF-7	breast:
5	chr7:100025389..100027922-chr7:100449017..100452017,3	K562	blood:
6	chr7:100422826..100425783-chr7:100447402..100452140,5	K562	blood:
7	chr7:100301473..100305247-chr7:100448414..100451828,11	MCF-7	breast:
8	chr7:100447367..100452420-chr7:100484839..100489079,9	MCF-7	breast:
9	chr7:100450060..100453457-chr7:100456779..100461941,7	MCF-7	breast:
10	chr7:100450052..100452622-chr7:100454484..100455985,2	K562	blood:
11	chr7:100423433..100426983-chr7:100448013..100452140,5	K562	blood:
12	chr7:100448750..100454655-chr7:100469427..100474218,6	MCF-7	breast:
13	chr7:100448977..100453392-chr7:100463620..100466806,5	K562	blood:
14	chr7:100449276..100451751-chr7:100451970..100455988,3	MCF-7	breast:
15	chr7:100450381..100452181-chr7:100471838..100473668,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000087077	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000172336	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12538287	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808356	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3847067	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4727465	0.80[AMR][1000 genomes]
rs4727468	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6955197	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7384255	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7782299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7789085	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800241	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12535629	FAM185A	cis	cerebellum	SCAN
rs12535629	TRRAP	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100450800-100454200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:100450800-100454400	Weak transcription	Aorta	Aorta
3	chr7:100451000-100451800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr7:100451000-100452000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:100451000-100452200	Weak transcription	Spleen	Spleen
6	chr7:100451000-100452400	Enhancers	Fetal Brain Male	brain
7	chr7:100451000-100452800	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:100451000-100453000	Weak transcription	Brain Substantia Nigra	brain
9	chr7:100451000-100453000	Weak transcription	Ovary	ovary
10	chr7:100451000-100453200	Weak transcription	Gastric	stomach
11	chr7:100451000-100458200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:100451000-100461200	Weak transcription	Stomach Mucosa	stomach
13	chr7:100451000-100463200	Weak transcription	HSMMtube	muscle
14	chr7:100451000-100464200	Weak transcription	Left Ventricle	heart
15	chr7:100451000-100464200	Weak transcription	Small Intestine	intestine
16	chr7:100451000-100464400	Weak transcription	Fetal Kidney	kidney
17	chr7:100451200-100451800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:100451200-100451800	Enhancers	Placenta	Placenta
19	chr7:100451200-100452000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:100451200-100452000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr7:100451200-100452000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:100451200-100452000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr7:100451200-100452000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr7:100451200-100452000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:100451200-100452000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:100451200-100452000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:100451200-100452000	Enhancers	Fetal Muscle Trunk	muscle
28	chr7:100451200-100452000	Weak transcription	Fetal Stomach	stomach
29	chr7:100451200-100452200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:100451200-100452200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:100451200-100452200	Enhancers	Primary hematopoietic stem cells	blood
32	chr7:100451200-100452200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:100451200-100452200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:100451200-100452200	Weak transcription	Esophagus	oesophagus
35	chr7:100451200-100452200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:100451200-100452200	Enhancers	Fetal Brain Female	brain
37	chr7:100451200-100452400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:100451200-100452400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:100451200-100452600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:100451200-100452800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:100451200-100453000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:100451200-100453000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:100451200-100453000	Weak transcription	NHLF	lung
44	chr7:100451200-100453200	Weak transcription	Brain Anterior Caudate	brain
45	chr7:100451200-100453200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:100451200-100453200	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:100451200-100454200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr7:100451200-100454400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:100451200-100454800	Weak transcription	Pancreas	Pancrea
50	chr7:100451200-100455200	Weak transcription	Rectal Smooth Muscle	rectum

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