Variant report

Variant	rs6662583
Chromosome Location	chr1:227383889-227383890
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	chr1:227383842..227386781-chr1:227388623..227390741,2	K562	blood:
2	chr1:227383751..227387113-chr1:227389765..227393443,4	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10495253	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10799381	0.83[AMR][1000 genomes]
rs10916080	0.83[AMR][1000 genomes]
rs10916104	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12039370	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12139758	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs1320494	0.83[AMR][1000 genomes]
rs1483	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1929858	0.80[AMR][1000 genomes]
rs2102634	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2482454	0.85[AMR][1000 genomes]
rs2492630	0.83[AMR][1000 genomes]
rs2670462	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2670471	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2718193	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2813947	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2813948	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2813950	0.84[ASW][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2813965	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2813967	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2813969	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2813970	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3754418	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4351610	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4500279	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4653479	0.83[AMR][1000 genomes]
rs4653813	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs485234	0.84[AMR][1000 genomes]
rs488104	0.85[AMR][1000 genomes]
rs498020	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs56219094	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61834571	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs648877	0.83[AMR][1000 genomes]
rs6682472	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682642	0.83[AMR][1000 genomes]
rs6685823	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs6692080	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6697665	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6699828	0.83[AMR][1000 genomes]
rs689094	0.85[AMR][1000 genomes]
rs694740	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs7412928	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7512409	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7521110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7521639	0.83[JPT][hapmap]
rs7523167	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7543579	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7549520	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]

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	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
6	esv3340979	chr1:227382729-227387327	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3369323	chr1:227383229-227386827	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6662583	MIXL1	cis	parietal	SCAN
rs6662583	ITPKB	cis	lymphoblastoid	seeQTL
rs6662583	C1orf65	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:227343200-227400400	Weak transcription	A549	lung
4	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
7	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
16	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
17	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
18	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
19	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:227373400-227397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
23	chr1:227374800-227391000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:227375200-227386800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:227375600-227410800	Weak transcription	HepG2	liver
26	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
27	chr1:227377000-227388800	Weak transcription	Small Intestine	intestine
28	chr1:227378000-227389400	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
30	chr1:227379000-227398000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:227379000-227398000	Weak transcription	Liver	Liver
32	chr1:227379600-227399200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227380200-227385800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:227380200-227385800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:227380200-227391200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:227380200-227405200	Weak transcription	Gastric	stomach
38	chr1:227380200-227421800	Weak transcription	Ovary	ovary
39	chr1:227380400-227385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:227380400-227385400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:227380400-227385800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:227380400-227385800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:227380400-227385800	Weak transcription	HSMM	muscle
44	chr1:227380400-227389000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:227380400-227389400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:227380400-227398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:227380400-227398000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:227380400-227400000	Weak transcription	HSMMtube	muscle
49	chr1:227380400-227400000	Weak transcription	NHEK	skin
50	chr1:227380400-227404000	Weak transcription	Muscle Satellite Cultured Cells	--

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