Variant report

Variant	rs6576968
Chromosome Location	chr2:96904127-96904128
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	POLR2A	chr2:96904075-96904152	K562	blood:	n/a	n/a
2	POLR2A	chr2:96903240-96904155	K562	blood:	n/a	n/a
3	POLR2A	chr2:96903426-96905671	K562	blood:	n/a	n/a
4	POLR2A	chr2:96903291-96904357	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:96901484-96904297	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96901752..96905157-chr2:96907799..96911905,3	K562	blood:

Variant related genes	Relation type
STARD7-AS1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11551400	0.83[GIH][hapmap];0.86[TSI][hapmap]
rs12617019	0.83[CEU][hapmap];0.94[GIH][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap]
rs17119615	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2276650	0.83[CEU][hapmap]
rs3852673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs4371393	0.83[CEU][hapmap];0.91[GIH][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap]
rs4592891	0.89[ASN][1000 genomes]
rs4826	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.95[ASN][1000 genomes]
rs56088823	0.91[AFR][1000 genomes]
rs57476471	1.00[ASN][1000 genomes]
rs59082429	0.90[ASN][1000 genomes]
rs59664047	0.95[ASN][1000 genomes]
rs60409279	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61624166	0.91[AFR][1000 genomes]
rs62152966	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62152972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153011	0.95[ASN][1000 genomes]
rs62153018	0.95[ASN][1000 genomes]
rs62153022	0.95[ASN][1000 genomes]
rs6756208	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72825854	0.95[ASN][1000 genomes]
rs72825856	0.95[ASN][1000 genomes]
rs72825864	0.95[ASN][1000 genomes]
rs73958180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579709	0.83[CEU][hapmap]
rs7580178	0.91[ASN][1000 genomes]
rs997547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997548	0.83[CEU][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv963665	chr2:96882253-96905611	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6576968	AC008268.2	cis	Artery Tibial	GTEx
rs6576968	AMOTL2	trans	parietal	SCAN
rs6576968	FER1L5	cis	parietal	SCAN
rs6576968	TMEM127	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96875000-96906200	Weak transcription	Esophagus	oesophagus
2	chr2:96875200-96905000	Weak transcription	Aorta	Aorta
3	chr2:96875600-96907000	Weak transcription	Fetal Thymus	thymus
4	chr2:96875800-96905800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:96876000-96904200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:96876000-96905800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:96876000-96906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:96876200-96905200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:96876200-96906000	Weak transcription	Osteobl	bone
11	chr2:96876200-96906600	Weak transcription	Brain Anterior Caudate	brain
12	chr2:96876200-96916000	Weak transcription	Dnd41	blood
13	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:96886000-96905400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:96886000-96905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:96886400-96905000	Weak transcription	Fetal Heart	heart
18	chr2:96886800-96905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:96887800-96905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:96888000-96905400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:96889600-96915800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:96891200-96916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:96891400-96916400	Weak transcription	HSMM	muscle
24	chr2:96891600-96905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:96891600-96906800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:96893200-96907600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:96896000-96906600	Weak transcription	Placenta	Placenta
28	chr2:96896000-96907800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:96896200-96905000	Weak transcription	Psoas Muscle	Psoas
30	chr2:96896200-96917600	Weak transcription	Pancreas	Pancrea
31	chr2:96896400-96905000	Weak transcription	Right Ventricle	heart
32	chr2:96896400-96905400	Weak transcription	Right Atrium	heart
33	chr2:96896600-96911200	Weak transcription	K562	blood
34	chr2:96897400-96906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:96897400-96906000	Weak transcription	HMEC	breast
36	chr2:96897400-96906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:96899400-96905200	Weak transcription	Fetal Brain Male	brain
38	chr2:96899600-96918800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:96900000-96905200	Weak transcription	Spleen	Spleen
40	chr2:96900000-96907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:96900000-96917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:96900200-96906200	Weak transcription	Liver	Liver
43	chr2:96900200-96907800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:96900400-96906400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:96900400-96917600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:96900600-96907000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:96900800-96905200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr2:96900800-96906600	Weak transcription	Primary B cells from cord blood	blood
49	chr2:96900800-96906600	Weak transcription	GM12878-XiMat	blood
50	chr2:96900800-96906800	Weak transcription	Primary B cells from peripheral blood	blood

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