Variant report

Variant	rs7623847
Chromosome Location	chr3:110918671-110918672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD96-4	chr3:110917882-110920289	NONHSAT091143

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13093206	0.83[AFR][1000 genomes]
rs1477841	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1477842	0.85[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1477843	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs1477846	0.85[CEU][hapmap];1.00[TSI][hapmap]
rs1477847	0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap]
rs1477848	0.85[CEU][hapmap];1.00[TSI][hapmap]
rs1477851	0.94[ASW][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs2126713	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs2399373	0.94[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs2399375	0.85[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4682033	0.84[AFR][1000 genomes]
rs4682034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682229	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4682230	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4682231	0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap]
rs4682234	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682238	0.85[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs55774570	0.84[AFR][1000 genomes]
rs56668317	0.84[AFR][1000 genomes]
rs57417964	0.84[AFR][1000 genomes]
rs6437948	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6437952	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6437953	0.85[CEU][hapmap];0.83[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs6437955	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66803420	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67209183	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786854	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6794645	0.85[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs7430600	0.94[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7610760	0.85[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs7612667	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7620372	0.82[CEU][hapmap]
rs7623880	0.85[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs7653595	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9821335	0.87[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs9828899	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs9866028	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876350	0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap]

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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:110853000-110919600	Weak transcription	Fetal Brain Male	brain
3	chr3:110869400-110929000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:110872600-110918800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:110881000-110928000	Weak transcription	Osteobl	bone
6	chr3:110890800-110919800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:110894000-110922800	Weak transcription	Gastric	stomach
8	chr3:110894000-110924000	Weak transcription	Fetal Stomach	stomach
9	chr3:110894000-110934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:110894200-110924800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:110894200-110925600	Weak transcription	NHLF	lung
12	chr3:110894200-110929600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:110899200-110935200	Weak transcription	Lung	lung
14	chr3:110903400-110929200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:110910200-110927200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:110911400-110919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:110912000-110923800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:110913000-110918800	Weak transcription	NHDF-Ad	bronchial
19	chr3:110913400-110918800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:110913400-110924200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:110913400-110932000	Weak transcription	Fetal Heart	heart
22	chr3:110914200-110924000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:110914200-110925800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:110914400-110921800	Weak transcription	Aorta	Aorta
25	chr3:110914400-110924200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:110914400-110924200	Weak transcription	Left Ventricle	heart
27	chr3:110914400-110928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:110914600-110919600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:110914600-110922000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:110914800-110918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:110915000-110924000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:110915000-110934200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:110915200-110919600	Weak transcription	Ovary	ovary
34	chr3:110915400-110928000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:110915600-110929800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:110916000-110928200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:110916200-110925600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:110916400-110924400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:110916600-110921200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:110916600-110923800	Weak transcription	Dnd41	blood
41	chr3:110916800-110923800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:110917000-110918800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:110917000-110919800	Weak transcription	A549	lung
44	chr3:110917000-110921000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:110917000-110921800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:110917000-110922600	Weak transcription	NH-A	brain
47	chr3:110917000-110923400	Weak transcription	Liver	Liver
48	chr3:110917000-110933400	Weak transcription	Placenta	Placenta
49	chr3:110917200-110924200	Weak transcription	Fetal Lung	lung
50	chr3:110917200-110929000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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