Variant report

Variant	rs6687946
Chromosome Location	chr1:185281739-185281740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr1:185281611-185281751	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:185281342-185281803	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:185281670-185281870	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185124975..185127830-chr1:185279297..185282140,2	K562	blood:

Variant related genes	Relation type
IVNS1ABP	TF binding region
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10489582	1.00[EUR][1000 genomes]
rs10494582	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798007	0.87[ASN][1000 genomes]
rs11802738	0.91[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11804954	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807870	0.84[LWK][hapmap]
rs11811583	0.97[AFR][1000 genomes]
rs12026308	1.00[EUR][1000 genomes]
rs12240005	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12240119	0.81[AMR][1000 genomes]
rs16823862	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823869	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823875	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823884	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823891	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2025228	1.00[EUR][1000 genomes]
rs3766713	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766716	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3895195	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41377350	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs57927210	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57960155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58031282	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58292874	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58685423	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59035619	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59227355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59611551	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59818790	1.00[EUR][1000 genomes]
rs60064915	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61537994	1.00[EUR][1000 genomes]
rs61573899	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6672580	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674689	0.84[ASW][hapmap];0.87[MKK][hapmap]
rs6679946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680028	0.90[YRI][hapmap];0.95[AFR][1000 genomes]
rs6695308	0.84[ASW][hapmap]
rs6698620	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs7515757	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7516303	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540216	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs7555243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs953701	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs953702	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185262000-185281800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:185262000-185281800	Strong transcription	HSMM	muscle
3	chr1:185268800-185284600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:185270400-185284800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:185270800-185284800	Weak transcription	Gastric	stomach
6	chr1:185274800-185283600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:185275000-185284800	Weak transcription	Esophagus	oesophagus
8	chr1:185275200-185284800	Weak transcription	Aorta	Aorta
9	chr1:185275600-185283400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:185275800-185285000	Weak transcription	Spleen	Spleen
11	chr1:185276400-185284600	Weak transcription	Lung	lung
12	chr1:185277000-185283400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:185277600-185283200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:185277600-185283400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:185277800-185283400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:185278200-185283800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:185278400-185282600	Weak transcription	Fetal Lung	lung
18	chr1:185278600-185281800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:185278800-185281800	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:185278800-185283400	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:185279000-185282600	Weak transcription	Right Atrium	heart
22	chr1:185279800-185281800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:185279800-185281800	Enhancers	Right Ventricle	heart
24	chr1:185279800-185283400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:185280000-185282600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:185280000-185282600	Enhancers	Fetal Intestine Small	intestine
27	chr1:185280000-185282600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:185280200-185281800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:185280200-185281800	Enhancers	Brain Germinal Matrix	brain
30	chr1:185280200-185282400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr1:185280200-185283200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:185280200-185283400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:185280400-185282000	Enhancers	Colon Smooth Muscle	Colon
34	chr1:185280400-185282400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:185280400-185282400	Weak transcription	HSMMtube	muscle
36	chr1:185280400-185282600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:185280400-185282600	Weak transcription	Ovary	ovary
38	chr1:185280400-185283000	Weak transcription	Left Ventricle	heart
39	chr1:185280400-185283200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:185280400-185283400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:185280400-185283600	Weak transcription	Placenta	Placenta
42	chr1:185280400-185283800	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:185280400-185284600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:185280400-185284600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:185280600-185281800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:185280600-185281800	Enhancers	Brain Substantia Nigra	brain
47	chr1:185280600-185281800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:185280600-185282000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:185280600-185282000	Flanking Active TSS	Fetal Brain Female	brain
50	chr1:185280600-185282200	Enhancers	Brain Inferior Temporal Lobe	brain

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