Variant report

Variant	rs10801589
Chromosome Location	chr1:197076194-197076195
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	chr1:197075217..197076795-chr1:197101256..197102905,2	K562	blood:
2	chr1:197075415..197078387-chr1:197103819..197106746,2	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484502	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10737685	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10754209	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10754216	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10801594	0.93[YRI][hapmap]
rs10922163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127661	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12755054	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs1332661	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1332667	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1412635	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1611982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1615413	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1750311	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs17550014	0.91[ASN][1000 genomes]
rs17550411	0.89[ASN][1000 genomes]
rs1759016	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap]
rs2298882	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2336596	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2878749	0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs3737110	0.89[ASN][1000 genomes]
rs3737111	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748557	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3762271	0.91[ASN][1000 genomes]
rs41304071	0.91[ASN][1000 genomes]
rs41308365	0.91[ASN][1000 genomes]
rs41310911	0.89[ASN][1000 genomes]
rs41310925	0.91[ASN][1000 genomes]
rs41310927	0.91[ASN][1000 genomes]
rs4244139	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56084994	0.91[ASN][1000 genomes]
rs5990	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5996	0.81[ASN][1000 genomes]
rs5998	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61819074	0.86[ASN][1000 genomes]
rs61819087	0.91[ASN][1000 genomes]
rs61819088	0.91[ASN][1000 genomes]
rs61819089	0.91[ASN][1000 genomes]
rs6677930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6690730	0.89[ASN][1000 genomes]
rs6700180	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702252	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs698859	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs72736469	0.81[ASN][1000 genomes]
rs72736474	0.81[ASN][1000 genomes]
rs7410943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7514071	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518773	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525490	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs857018	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955927	0.86[ASN][1000 genomes]
rs9727516	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873065	chr1:197027749-197076194	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv873068	chr1:197046782-197076194	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv873069	chr1:197055925-197109042	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10801589	F13B	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197076200	Weak transcription	NHLF	lung
2	chr1:197052200-197083600	Weak transcription	Fetal Stomach	stomach
3	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
6	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
7	chr1:197066600-197083600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:197067000-197092200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:197070200-197076400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr1:197070600-197076200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr1:197070600-197100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:197070800-197078000	Strong transcription	Fetal Thymus	thymus
13	chr1:197070800-197085400	Weak transcription	Osteobl	bone
14	chr1:197071000-197084400	Weak transcription	Fetal Heart	heart
15	chr1:197071000-197105400	Strong transcription	Dnd41	blood
16	chr1:197071200-197077400	Strong transcription	Fetal Lung	lung
17	chr1:197071400-197095800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:197071600-197077800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:197071800-197104600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:197072000-197076400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:197072400-197078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:197072600-197078400	Strong transcription	A549	lung
23	chr1:197072600-197087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:197072600-197104600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:197072600-197107400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:197072800-197077200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:197072800-197078600	Strong transcription	Hela-S3	cervix
28	chr1:197073000-197076600	Strong transcription	HMEC	breast
29	chr1:197073000-197078000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:197073000-197079600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:197073000-197104000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:197073200-197078200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:197073400-197077000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:197073400-197078600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:197073600-197098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:197073800-197083400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:197073800-197085200	Weak transcription	GM12878-XiMat	blood
39	chr1:197073800-197091400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:197074000-197076800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:197074000-197077400	Weak transcription	HUVEC	blood vessel
42	chr1:197074000-197077800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:197074000-197078000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:197074000-197080000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:197074000-197085400	Weak transcription	HepG2	liver
46	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
47	chr1:197074200-197077800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:197074200-197078200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:197074200-197085000	Weak transcription	NHDF-Ad	bronchial
50	chr1:197074200-197091400	Weak transcription	NHEK	skin

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