Variant report

Variant	rs902780
Chromosome Location	chr6:119108363-119108364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119104519..119106736-chr6:119106969..119109771,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1022707	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1022708	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs11153782	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1885125	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2145569	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs284919	0.84[JPT][hapmap]
rs4946372	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4946373	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4946382	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs6904381	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs6912082	0.83[ASN][1000 genomes]
rs6912762	0.84[ASN][1000 genomes]
rs6918844	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6939937	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs7381535	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7743045	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7754916	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320671	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs9374747	0.81[ASN][1000 genomes]
rs9387621	0.84[CHB][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs9401106	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs9489520	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active 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	10 gene(s)	inside rSNPs	diseases
6	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv886568	chr6:119044453-119132164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv886569	chr6:119055873-119132164	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	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
rs902780	ASF1A	Cis_1M	lymphoblastoid	RTeQTL
rs902780	MCM9	cis	lymphoblastoid	seeQTL
rs902780	MCM9	cis	cerebellum	SCAN
rs902780	C6orf204	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119098800-119108800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:119104800-119109000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:119105400-119110400	Weak transcription	HSMMtube	muscle
4	chr6:119105800-119108400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:119106200-119108800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:119106200-119108800	Weak transcription	Adipose Nuclei	Adipose
7	chr6:119106200-119113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:119106200-119113600	Weak transcription	Fetal Intestine Small	intestine
9	chr6:119106400-119109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:119106400-119109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:119106400-119109400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:119106400-119109400	Weak transcription	Left Ventricle	heart
13	chr6:119106400-119110600	Weak transcription	Lung	lung
14	chr6:119106800-119108600	Weak transcription	Brain Angular Gyrus	brain
15	chr6:119106800-119109000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:119106800-119109400	Weak transcription	Placenta	Placenta
17	chr6:119106800-119110000	Weak transcription	Right Atrium	heart
18	chr6:119106800-119110400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:119106800-119110600	Weak transcription	Brain Anterior Caudate	brain
20	chr6:119107000-119109000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:119107000-119109000	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:119107000-119109000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:119107000-119110400	Weak transcription	Fetal Brain Male	brain
24	chr6:119107200-119108800	Weak transcription	Fetal Lung	lung
25	chr6:119107600-119108400	Enhancers	Fetal Stomach	stomach
26	chr6:119107800-119110600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:119107800-119111400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:119108000-119108800	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:119108000-119109000	Enhancers	Gastric	stomach
30	chr6:119108000-119109000	Enhancers	Stomach Mucosa	stomach
31	chr6:119108000-119109600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:119108000-119109600	Enhancers	Brain Substantia Nigra	brain
33	chr6:119108000-119109800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:119108000-119109800	Enhancers	Brain Hippocampus Middle	brain
35	chr6:119108000-119110600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:119108000-119110800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr6:119108200-119108400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:119108200-119108800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr6:119108200-119109800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:119108200-119109800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:119108200-119110800	Enhancers	Primary T helper cells fromperipheralblood	blood

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