Variant report

Variant	rs3778409
Chromosome Location	chr6:166954244-166954245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10214537	1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12528147	0.84[ASN][1000 genomes]
rs12528167	1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs35302651	0.83[ASN][1000 genomes]
rs3757193	1.00[YRI][hapmap]
rs3778412	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778418	1.00[YRI][hapmap]
rs3778422	1.00[YRI][hapmap]
rs3799632	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3799647	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799654	0.86[ASN][1000 genomes]
rs3799658	1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs3799670	1.00[YRI][hapmap]
rs55665778	0.83[ASN][1000 genomes]
rs9364856	1.00[YRI][hapmap]
rs9457174	1.00[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:166929600-166955600	Weak transcription	HMEC	breast
4	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:166935400-166966400	Weak transcription	NH-A	brain
6	chr6:166938200-166955800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:166941000-166954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:166941400-166954600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:166941400-166955600	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:166941800-166954800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:166944200-166954800	Weak transcription	Stomach Mucosa	stomach
12	chr6:166944400-166954800	Weak transcription	Colonic Mucosa	Colon
13	chr6:166944600-166955600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:166944600-166957200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:166944600-166958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:166947200-166954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:166947200-166955000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:166947400-166969400	Weak transcription	Aorta	Aorta
19	chr6:166948600-166954600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:166949600-166954600	Weak transcription	Spleen	Spleen
21	chr6:166949600-166954800	Weak transcription	Pancreas	Pancrea
22	chr6:166949800-166954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:166949800-166955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:166949800-166955800	Weak transcription	NHLF	lung
25	chr6:166949800-166956800	Weak transcription	Right Ventricle	heart
26	chr6:166949800-166964800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:166950000-166955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:166950200-166954400	Weak transcription	Brain Germinal Matrix	brain
29	chr6:166950200-166954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:166950200-166954600	Weak transcription	Gastric	stomach
31	chr6:166950200-166954600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:166950200-166960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:166950800-166958600	Weak transcription	NHDF-Ad	bronchial
34	chr6:166951600-166955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:166951800-166954400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:166951800-166959000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:166952000-166954400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:166952000-166954600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:166952000-166954800	Weak transcription	Ovary	ovary
40	chr6:166952000-166955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:166952000-166955800	Weak transcription	HUVEC	blood vessel
42	chr6:166952000-166957000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:166952200-166954400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:166952400-166954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:166952400-166954600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:166952400-166954600	Weak transcription	Lung	lung
47	chr6:166952400-166954600	Weak transcription	Osteobl	bone
48	chr6:166952400-166957200	Weak transcription	Fetal Brain Male	brain
49	chr6:166952400-166969000	Weak transcription	Psoas Muscle	Psoas
50	chr6:166952800-166954400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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