Variant report

Variant	rs10409408
Chromosome Location	chr19:18611895-18611896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18557694..18558324-chr19:18611401..18611905,2	MCF-7	breast:
2	chr19:18611870..18615199-chr19:18629842..18634728,4	MCF-7	breast:
3	chr19:18606016..18607670-chr19:18611209..18613492,2	MCF-7	breast:
4	chr19:18609822..18612053-chr19:18615646..18618290,2	MCF-7	breast:
5	chr19:18610356..18612119-chr19:18654101..18656903,2	MCF-7	breast:
6	chr19:18604114..18606153-chr19:18610704..18612902,2	MCF-7	breast:
7	chr19:18611587..18620542-chr19:18622883..18629236,13	MCF-7	breast:
8	chr19:18606523..18611350-chr19:18611496..18616522,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction
ENSG00000105701	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10164323	0.86[JPT][hapmap]
rs10402322	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409346	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410797	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10413922	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10416993	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418331	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10423802	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045631	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086110	0.81[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs11668704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670392	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672385	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11879757	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980726	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982295	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12983263	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469412	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469413	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971093	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013069	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303692	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28534973	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2891676	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213500	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35004712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35742476	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4006662	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4303657	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580317	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808135	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808802	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808803	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808805	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808807	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808811	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808812	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808813	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55715336	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57923655	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6512269	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512270	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512271	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246788	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247540	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249760	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251232	0.85[EUR][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252185	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255936	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7256530	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258891	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7259135	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507218	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100343	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8102717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104247	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106068	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106332	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111397	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111582	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111824	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112372	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112859	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888668	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888669	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
2	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
6	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10409408	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10409408	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18594000-18621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:18600400-18630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:18600600-18619800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:18602200-18621400	Enhancers	Right Ventricle	heart
5	chr19:18602600-18621400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:18602800-18612600	Enhancers	Placenta	Placenta
7	chr19:18603600-18622600	Enhancers	Psoas Muscle	Psoas
8	chr19:18604200-18619000	Enhancers	Fetal Thymus	thymus
9	chr19:18604800-18618400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr19:18605400-18621800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:18606800-18614600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:18606800-18625800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:18607000-18615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:18607200-18617800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:18607600-18617600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr19:18607600-18618000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:18607600-18621600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr19:18607600-18622400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:18607800-18612200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:18607800-18614400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:18608000-18614800	Weak transcription	Fetal Kidney	kidney
22	chr19:18608000-18615800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:18608400-18612400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:18608400-18612600	Weak transcription	Stomach Mucosa	stomach
25	chr19:18608400-18613600	Weak transcription	HepG2	liver
26	chr19:18608400-18613800	Weak transcription	HMEC	breast
27	chr19:18608400-18617200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:18608400-18617200	Weak transcription	K562	blood
29	chr19:18609000-18612000	Enhancers	Duodenum Mucosa	Duodenum
30	chr19:18609000-18615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:18609200-18613000	Enhancers	Colon Smooth Muscle	Colon
32	chr19:18609200-18613000	Enhancers	Ovary	ovary
33	chr19:18609200-18614200	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr19:18609200-18617800	Enhancers	Adipose Nuclei	Adipose
35	chr19:18609200-18619600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr19:18609200-18620800	Enhancers	Brain Hippocampus Middle	brain
37	chr19:18609200-18621400	Enhancers	Fetal Muscle Trunk	muscle
38	chr19:18609200-18621400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:18609200-18621400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr19:18609200-18621600	Enhancers	Liver	Liver
41	chr19:18609200-18621600	Enhancers	Left Ventricle	heart
42	chr19:18609400-18613000	Enhancers	Colonic Mucosa	Colon
43	chr19:18609400-18618400	Weak transcription	Thymus	Thymus
44	chr19:18609400-18621400	Enhancers	Lung	lung
45	chr19:18609400-18621600	Enhancers	Pancreas	Pancrea
46	chr19:18609800-18612000	Enhancers	NHDF-Ad	bronchial
47	chr19:18609800-18612200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:18609800-18620200	Enhancers	Gastric	stomach
49	chr19:18609800-18621000	Enhancers	Fetal Muscle Leg	muscle
50	chr19:18609800-18621400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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