Variant report

Variant	rs6812991
Chromosome Location	chr4:48047591-48047592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48043679..48046228-chr4:48047228..48049577,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1003873	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs11733284	0.83[JPT][hapmap]
rs11736427	0.83[JPT][hapmap]
rs13116684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120847	0.83[JPT][hapmap]
rs13121957	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13145218	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146880	0.82[JPT][hapmap]
rs13150783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151608	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1567217	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs224799	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279965	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs321622	0.82[JPT][hapmap];0.80[AFR][1000 genomes]
rs321630	0.82[JPT][hapmap]
rs321631	0.82[JPT][hapmap]
rs321632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs321634	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321635	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35085584	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695325	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55670663	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447609	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832503	0.82[JPT][hapmap]
rs7674929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6812991	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
2	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
3	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
4	chr4:48038000-48047800	Weak transcription	NHEK	skin
5	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:48041600-48053000	Weak transcription	HMEC	breast
7	chr4:48044600-48049200	Enhancers	Primary B cells from cord blood	blood
8	chr4:48044800-48049200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:48044800-48049400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:48045000-48049200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:48045000-48049400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:48045000-48049400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:48045200-48048200	Enhancers	Stomach Mucosa	stomach
14	chr4:48045200-48049000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:48045400-48052200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:48045600-48047800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:48045600-48048200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:48045600-48048200	Weak transcription	Fetal Heart	heart
19	chr4:48045800-48047800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr4:48045800-48048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:48045800-48048800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr4:48045800-48049000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:48045800-48049400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:48045800-48049600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:48045800-48052600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:48046000-48047600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:48046000-48049000	Weak transcription	Liver	Liver
28	chr4:48046000-48049200	Weak transcription	HepG2	liver
29	chr4:48046000-48049600	Weak transcription	Fetal Intestine Small	intestine
30	chr4:48046200-48049400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr4:48046400-48049000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr4:48046400-48049200	Enhancers	Primary T cells from cord blood	blood
33	chr4:48046400-48050400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:48046600-48049000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr4:48046800-48047800	Enhancers	GM12878-XiMat	blood
36	chr4:48047000-48048000	Weak transcription	Fetal Thymus	thymus
37	chr4:48047200-48048200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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