Variant report

Variant	rs6050796
Chromosome Location	chr20:25678737-25678738
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	SREBP1	chr20:25676527-25679236	GM12878	blood:	n/a	n/a
2	MAX	chr20:25678611-25678858	NB4	blood:	n/a	chr20:25678699-25678709
3	STAT3	chr20:25678658-25678806	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25603699..25606216-chr20:25676779..25679090,3	MCF-7	breast:
2	chr20:25602422..25607796-chr20:25675112..25679388,9	K562	blood:

Variant related genes	Relation type
ZNF337	TF binding region
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 175 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10485776	1.00[JPT][hapmap]
rs1109100	1.00[JPT][hapmap]
rs1122769	1.00[JPT][hapmap]
rs12106173	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1569617	1.00[JPT][hapmap]
rs16987789	1.00[JPT][hapmap]
rs16987799	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs16987820	1.00[JPT][hapmap]
rs16987934	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs16988014	1.00[JPT][hapmap]
rs1883528	1.00[JPT][hapmap]
rs2103661	0.85[JPT][hapmap]
rs2179458	1.00[JPT][hapmap]
rs2387977	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2388026	0.86[ASN][1000 genomes]
rs242130	0.81[CHD][hapmap]
rs242133	1.00[JPT][hapmap]
rs35516971	0.81[ASN][1000 genomes]
rs3764695	0.86[ASN][1000 genomes]
rs3813916	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs402120	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4098823	0.86[ASN][1000 genomes]
rs4098824	0.86[ASN][1000 genomes]
rs4113658	0.86[ASN][1000 genomes]
rs4113659	0.86[ASN][1000 genomes]
rs4113661	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113662	0.86[ASN][1000 genomes]
rs41308623	0.81[ASN][1000 genomes]
rs426563	1.00[JPT][hapmap]
rs4318454	0.84[ASN][1000 genomes]
rs4343537	0.86[ASN][1000 genomes]
rs4368405	0.84[ASN][1000 genomes]
rs447808	1.00[JPT][hapmap]
rs4574179	0.86[ASN][1000 genomes]
rs4813579	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815436	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4815438	0.83[ASW][hapmap];0.86[LWK][hapmap]
rs4815445	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815450	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57638633	0.86[ASN][1000 genomes]
rs59399848	0.84[ASN][1000 genomes]
rs6037131	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6037133	1.00[JPT][hapmap]
rs6037159	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037161	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037164	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037166	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037167	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037168	0.81[ASN][1000 genomes]
rs6037169	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6037179	0.86[ASN][1000 genomes]
rs6037180	0.86[ASN][1000 genomes]
rs6037193	0.86[ASN][1000 genomes]
rs6037195	0.82[JPT][hapmap]
rs6037196	1.00[JPT][hapmap]
rs6037198	0.86[ASN][1000 genomes]
rs6037199	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6037204	0.81[ASN][1000 genomes]
rs6037206	0.84[ASN][1000 genomes]
rs6037208	0.86[ASN][1000 genomes]
rs6037212	0.86[ASN][1000 genomes]
rs6037217	0.86[ASN][1000 genomes]
rs6037220	0.86[ASN][1000 genomes]
rs6037222	0.82[JPT][hapmap]
rs6037223	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs60463280	0.84[ASN][1000 genomes]
rs6050663	1.00[JPT][hapmap]
rs6050707	0.81[ASN][1000 genomes]
rs6050709	0.81[ASN][1000 genomes]
rs6050710	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050712	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050714	0.81[ASN][1000 genomes]
rs6050717	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050720	0.81[ASN][1000 genomes]
rs6050723	0.81[ASN][1000 genomes]
rs6050724	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050725	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050726	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050727	0.81[ASN][1000 genomes]
rs6050729	0.81[ASN][1000 genomes]
rs6050730	0.81[ASN][1000 genomes]
rs6050732	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050733	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050737	0.81[ASN][1000 genomes]
rs6050743	0.81[ASN][1000 genomes]
rs6050745	0.86[ASN][1000 genomes]
rs6050749	0.86[ASN][1000 genomes]
rs6050753	0.86[ASN][1000 genomes]
rs6050754	0.86[ASN][1000 genomes]
rs6050755	0.86[ASN][1000 genomes]
rs6050756	0.86[ASN][1000 genomes]
rs6050757	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050758	0.86[ASN][1000 genomes]
rs6050760	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050763	0.81[ASN][1000 genomes]
rs6050765	0.86[ASN][1000 genomes]
rs6050767	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050768	0.86[ASN][1000 genomes]
rs6050770	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050775	0.86[ASN][1000 genomes]
rs6050779	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050787	0.86[ASN][1000 genomes]
rs6050788	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050789	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050795	0.86[ASN][1000 genomes]
rs6050799	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050801	0.84[ASN][1000 genomes]
rs6050802	0.86[ASN][1000 genomes]
rs6050804	0.86[ASN][1000 genomes]
rs6050805	0.84[ASN][1000 genomes]
rs6050807	0.84[ASN][1000 genomes]
rs6050809	0.86[ASN][1000 genomes]
rs6050814	0.82[AFR][1000 genomes]
rs6050832	0.86[ASN][1000 genomes]
rs6050833	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050834	0.86[ASN][1000 genomes]
rs6050835	0.86[ASN][1000 genomes]
rs6050838	0.86[ASN][1000 genomes]
rs6050840	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050841	0.86[ASN][1000 genomes]
rs6050846	0.86[ASN][1000 genomes]
rs6050847	0.86[ASN][1000 genomes]
rs6050848	0.86[ASN][1000 genomes]
rs6050851	0.86[ASN][1000 genomes]
rs6050853	0.86[ASN][1000 genomes]
rs6050854	0.86[ASN][1000 genomes]
rs6050858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050867	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6083886	1.00[JPT][hapmap]
rs6083896	1.00[JPT][hapmap]
rs6083897	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs6083899	1.00[JPT][hapmap]
rs61052177	0.84[ASN][1000 genomes]
rs6115200	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115214	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6115215	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6115224	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115232	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132848	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6132850	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6138588	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6138600	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138612	1.00[JPT][hapmap]
rs7266130	1.00[JPT][hapmap]
rs7266592	1.00[JPT][hapmap]
rs73341361	0.86[ASN][1000 genomes]
rs73341363	0.84[ASN][1000 genomes]
rs73341365	0.84[ASN][1000 genomes]
rs73341397	0.86[ASN][1000 genomes]
rs73343217	0.86[ASN][1000 genomes]
rs73343255	0.86[ASN][1000 genomes]
rs73343275	0.84[ASN][1000 genomes]
rs73343292	0.84[ASN][1000 genomes]
rs73345232	0.86[ASN][1000 genomes]
rs7346687	0.86[ASN][1000 genomes]
rs742435	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs8115742	1.00[JPT][hapmap]
rs8116267	1.00[JPT][hapmap]
rs8117181	1.00[JPT][hapmap]
rs8120065	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8120594	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8121013	0.81[ASN][1000 genomes]
rs8121648	1.00[JPT][hapmap]
rs8126236	0.81[ASN][1000 genomes]
rs926486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926487	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs928121	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9753575	0.86[ASN][1000 genomes]
rs981440	0.86[ASN][1000 genomes]
rs981441	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3486652	chr20:25678552-25682550	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6050796	ZNF337	cis	lung	GTEx
rs6050796	RP4-694B14.5	cis	Thyroid	GTEx
rs6050796	NINL	cis	Nerve Tibial	GTEx
rs6050796	ZNF337	cis	Stomach	GTEx
rs6050796	RP4-694B14.5	cis	lung	GTEx
rs6050796	ZNF337	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25676000-25678800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:25676600-25678800	Active TSS	Brain Germinal Matrix	brain
3	chr20:25676600-25679200	Active TSS	GM12878-XiMat	blood
4	chr20:25677800-25678800	Active TSS	Fetal Brain Male	brain
5	chr20:25677800-25701000	Weak transcription	Pancreas	Pancrea
6	chr20:25678000-25678800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr20:25678000-25678800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr20:25678000-25678800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:25678000-25678800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:25678000-25678800	Enhancers	Brain Angular Gyrus	brain
11	chr20:25678000-25679000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr20:25678000-25679000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr20:25678000-25679000	Flanking Active TSS	Dnd41	blood
14	chr20:25678000-25679600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:25678000-25679600	Enhancers	Liver	Liver
16	chr20:25678000-25681600	Weak transcription	Brain Hippocampus Middle	brain
17	chr20:25678000-25687600	Weak transcription	Esophagus	oesophagus
18	chr20:25678400-25678800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr20:25678400-25678800	Enhancers	Right Atrium	heart
20	chr20:25678400-25678800	Enhancers	NHEK	skin
21	chr20:25678400-25679200	Enhancers	Fetal Brain Female	brain
22	chr20:25678400-25679200	Enhancers	HepG2	liver
23	chr20:25678600-25678800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr20:25678600-25678800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:25678600-25678800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr20:25678600-25678800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr20:25678600-25678800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:25678600-25678800	Enhancers	Fetal Kidney	kidney
29	chr20:25678600-25678800	Enhancers	Psoas Muscle	Psoas
30	chr20:25678600-25678800	Enhancers	Right Ventricle	heart
31	chr20:25678600-25678800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr20:25678600-25678800	Enhancers	Stomach Mucosa	stomach
33	chr20:25678600-25678800	Enhancers	Thymus	Thymus
34	chr20:25678600-25678800	Enhancers	Spleen	Spleen
35	chr20:25678600-25678800	Flanking Active TSS	A549	lung
36	chr20:25678600-25678800	Enhancers	Hela-S3	cervix
37	chr20:25678600-25678800	Flanking Active TSS	HMEC	breast
38	chr20:25678600-25678800	Enhancers	HSMMtube	muscle

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