Variant report

Variant	rs4804
Chromosome Location	chr1:212619339-212619340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212607004..212608669-chr1:212617399..212619627,2	MCF-7	breast:
2	chr1:212617519..212622581-chr1:212622841..212626048,6	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs3767871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472463	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479564	0.83[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs479807	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs483954	0.93[EUR][1000 genomes]
rs508432	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514362	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs521469	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527840	0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534186	0.86[ASN][1000 genomes]
rs575025	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577671	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs583058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs595066	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600016	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6540741	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs676490	0.91[ASN][1000 genomes]
rs681005	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs694274	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4804	TMEM206	cis	cerebellum	SCAN
rs4804	NENF	cis	Esophagus Mucosa	GTEx
rs4804	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs4804	TMEM206	cis	Esophagus Mucosa	GTEx
rs4804	CD34	cis	cerebellum	SCAN
rs4804	LGTN	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212607000-212623400	Weak transcription	HSMMtube	muscle
2	chr1:212607400-212622800	Weak transcription	Primary B cells from cord blood	blood
3	chr1:212607400-212625800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:212607400-212626000	Weak transcription	Colonic Mucosa	Colon
5	chr1:212607400-212629200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:212607600-212620600	Weak transcription	HMEC	breast
7	chr1:212607600-212621800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:212607600-212624000	Weak transcription	Fetal Brain Male	brain
9	chr1:212607600-212625800	Weak transcription	Stomach Mucosa	stomach
10	chr1:212607600-212626000	Weak transcription	NH-A	brain
11	chr1:212607800-212620000	Weak transcription	Osteobl	bone
12	chr1:212607800-212623400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:212607800-212624400	Weak transcription	NHEK	skin
14	chr1:212607800-212625800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:212607800-212625800	Weak transcription	NHLF	lung
16	chr1:212607800-212629400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:212608000-212621600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:212608000-212625800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:212608000-212627000	Weak transcription	HepG2	liver
20	chr1:212610800-212619800	Weak transcription	Hela-S3	cervix
21	chr1:212611000-212622200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:212613400-212621600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:212614200-212626000	Weak transcription	Fetal Kidney	kidney
24	chr1:212614400-212619800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:212614400-212626200	Weak transcription	Pancreas	Pancrea
26	chr1:212614400-212629200	Weak transcription	GM12878-XiMat	blood
27	chr1:212614400-212636800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:212614600-212622400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:212615000-212623400	Weak transcription	Right Atrium	heart
30	chr1:212615000-212623600	Weak transcription	Psoas Muscle	Psoas
31	chr1:212615800-212621400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:212616000-212621200	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:212616200-212620400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:212616600-212620200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:212616600-212621200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:212616800-212620800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:212616800-212621000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:212616800-212621200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:212616800-212621400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:212616800-212624000	Strong transcription	Fetal Intestine Small	intestine
41	chr1:212617200-212620200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:212617400-212619600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:212617400-212619600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:212617400-212619800	Strong transcription	Liver	Liver
45	chr1:212617400-212620000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:212617400-212620400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:212617400-212620800	Strong transcription	Fetal Intestine Large	intestine
48	chr1:212617400-212620800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:212617400-212621200	Strong transcription	Ovary	ovary
50	chr1:212617400-212621600	Strong transcription	Fetal Stomach	stomach

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