Variant report

Variant	rs1613209
Chromosome Location	chr1:247035179-247035180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247030122..247032370-chr1:247032584..247035559,2	K562	blood:
2	chr1:247033154..247036008-chr1:247106994..247108758,2	MCF-7	breast:
3	chr1:247017685..247021797-chr1:247033247..247038806,7	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1039009	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1039010	0.91[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11579381	0.81[JPT][hapmap]
rs11585741	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1472275	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1612610	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1619941	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs1691240	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1691241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1691252	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1691254	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1691255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1779964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779968	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1779969	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2172796	0.93[EUR][1000 genomes]
rs2642975	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs2642977	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2642990	0.81[EUR][1000 genomes]
rs2642991	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2800214	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2800215	0.88[EUR][1000 genomes]
rs2800219	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2800220	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800221	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818888	0.91[EUR][1000 genomes]
rs4971278	0.86[JPT][hapmap]
rs7542895	0.94[EUR][1000 genomes]
rs768197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs903461	0.81[JPT][hapmap]
rs9729306	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9729316	0.83[EUR][1000 genomes];0.82[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	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
6	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv5276	chr1:247028364-247073098	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1613209	SCCPDH	cis	lymphoblastoid	seeQTL
rs1613209	ZNF124	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247002000-247038200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:247002800-247043200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:247003200-247042200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:247003200-247042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:247003400-247043000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:247003400-247044600	Strong transcription	Dnd41	blood
9	chr1:247004000-247040800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:247004000-247041200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:247004000-247042800	Strong transcription	Primary T cells from cord blood	blood
12	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:247004200-247042400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:247004200-247042800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:247004200-247043000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:247004200-247044400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:247004200-247044400	Strong transcription	Liver	Liver
18	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:247004400-247043000	Strong transcription	Adipose Nuclei	Adipose
20	chr1:247004400-247044600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:247005200-247079800	Weak transcription	Stomach Mucosa	stomach
22	chr1:247006600-247071600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:247010000-247041200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:247018400-247056400	Weak transcription	Fetal Heart	heart
25	chr1:247020400-247072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:247022000-247043000	Strong transcription	A549	lung
27	chr1:247022400-247042800	Weak transcription	Gastric	stomach
28	chr1:247023400-247040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:247023600-247038800	Weak transcription	Right Ventricle	heart
30	chr1:247024200-247038400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:247024200-247052000	Weak transcription	Pancreas	Pancrea
32	chr1:247025200-247037000	Weak transcription	Brain Angular Gyrus	brain
33	chr1:247025200-247048000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:247025200-247052000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:247026400-247036400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:247026600-247039200	Strong transcription	Fetal Intestine Large	intestine
37	chr1:247026600-247040400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:247026800-247041600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:247027200-247035400	Weak transcription	HUVEC	blood vessel
40	chr1:247027800-247038800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:247028600-247040400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:247028600-247040400	Strong transcription	Fetal Lung	lung
43	chr1:247030000-247037400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:247030000-247041200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:247030000-247043000	Strong transcription	Fetal Thymus	thymus
46	chr1:247030000-247043200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:247030600-247042000	Strong transcription	Primary B cells from cord blood	blood
48	chr1:247030600-247042800	Strong transcription	HepG2	liver
49	chr1:247031200-247037400	Strong transcription	Fetal Intestine Small	intestine
50	chr1:247031200-247043800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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