Variant report

Variant	rs2813969
Chromosome Location	chr1:227404082-227404083
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	chr1:227400709..227402426-chr1:227403946..227405462,2	K562	blood:
2	chr1:227402647..227405396-chr1:227406531..227409406,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10495253	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916104	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12039370	0.83[EUR][1000 genomes]
rs12139758	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs1483	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2102634	0.82[EUR][1000 genomes]
rs2482454	0.80[AMR][1000 genomes]
rs2670462	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2670471	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718193	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2813947	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2813948	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2813950	0.94[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813965	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813967	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813970	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754418	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4351610	0.82[EUR][1000 genomes]
rs4500279	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4653813	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs488104	0.80[AMR][1000 genomes]
rs498020	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs56219094	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834571	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6662583	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682472	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685823	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs6692080	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697665	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689094	0.80[AMR][1000 genomes]
rs694740	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs7412928	0.83[EUR][1000 genomes]
rs7512409	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7521110	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521639	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7523167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549520	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2813969	ITPKB	cis	lymphoblastoid	seeQTL
rs2813969	MIXL1	cis	parietal	SCAN
rs2813969	C1orf65	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
4	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:227375600-227410800	Weak transcription	HepG2	liver
8	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
9	chr1:227380200-227405200	Weak transcription	Gastric	stomach
10	chr1:227380200-227421800	Weak transcription	Ovary	ovary
11	chr1:227380400-227406800	Weak transcription	NHDF-Ad	bronchial
12	chr1:227381600-227406600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
16	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:227386800-227406600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
21	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:227397000-227406800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:227398200-227413600	Weak transcription	NHLF	lung
24	chr1:227398600-227407000	Weak transcription	Lung	lung
25	chr1:227398800-227405600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:227398800-227407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:227398800-227411200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:227398800-227413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:227399000-227406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:227399000-227406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:227399000-227408800	Weak transcription	Liver	Liver
32	chr1:227399200-227406800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:227399200-227407000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:227399400-227411200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:227399400-227415400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:227399600-227413200	Weak transcription	HSMM	muscle
37	chr1:227399800-227407000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:227399800-227411000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:227400400-227406600	Weak transcription	Fetal Intestine Large	intestine
40	chr1:227400400-227406600	Weak transcription	Right Ventricle	heart
41	chr1:227400400-227407600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:227400400-227408200	Weak transcription	K562	blood
43	chr1:227400400-227410800	Weak transcription	Brain Angular Gyrus	brain
44	chr1:227400400-227410800	Weak transcription	Brain Substantia Nigra	brain
45	chr1:227400400-227413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:227400400-227413000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227400600-227413000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:227400600-227413000	Weak transcription	NHEK	skin
50	chr1:227400800-227412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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