Variant report

Variant	rs66530931
Chromosome Location	chr1:224689853-224689854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224683423..224687942-chr1:224688283..224691740,8	K562	blood:
2	chr1:224688139..224690298-chr1:225044581..225047366,2	K562	blood:
3	chr1:224348304..224349923-chr1:224689007..224690690,2	K562	blood:
4	chr1:224688210..224692730-chr1:224708810..224713777,4	K562	blood:
5	chr1:224622250..224624534-chr1:224688167..224691066,2	MCF-7	breast:
6	chr1:224645897..224648212-chr1:224688548..224690344,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10753467	0.80[EUR][1000 genomes]
rs10753468	0.80[EUR][1000 genomes]
rs11577170	0.80[EUR][1000 genomes]
rs11578709	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11584057	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11800613	0.80[EUR][1000 genomes]
rs12062871	0.82[EUR][1000 genomes]
rs12731630	0.80[EUR][1000 genomes]
rs12743200	0.80[EUR][1000 genomes]
rs12758579	0.80[EUR][1000 genomes]
rs16848365	0.80[EUR][1000 genomes]
rs17570292	0.90[EUR][1000 genomes]
rs2185684	0.80[EUR][1000 genomes]
rs34119581	0.86[ASN][1000 genomes]
rs35067427	0.80[EUR][1000 genomes]
rs35804313	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs6426134	0.86[ASN][1000 genomes]
rs6663522	0.80[EUR][1000 genomes]
rs6678608	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682205	0.86[ASN][1000 genomes]
rs6698343	0.90[EUR][1000 genomes]
rs67267495	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	0.80[EUR][1000 genomes]
rs885606	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66530931	CNIH4	cis	Esophagus Muscularis	GTEx
rs66530931	CNIH4	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224682800-224690200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:224685200-224695800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:224686000-224690000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:224686600-224690000	Weak transcription	Aorta	Aorta
5	chr1:224686600-224690000	Weak transcription	Liver	Liver
6	chr1:224686600-224690200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:224686600-224690200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:224686600-224691000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:224686600-224691000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:224686600-224691200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:224686600-224691200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:224686800-224690000	Weak transcription	Ovary	ovary
13	chr1:224686800-224690000	Weak transcription	Psoas Muscle	Psoas
14	chr1:224686800-224690000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:224686800-224690000	Weak transcription	Spleen	Spleen
16	chr1:224686800-224690200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:224686800-224690200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:224686800-224690600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:224686800-224691000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:224686800-224691000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:224686800-224691000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:224687200-224690000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:224687200-224690000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:224687200-224690000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:224687200-224690000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:224687200-224690000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:224687200-224690000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:224687200-224690000	Weak transcription	Placenta	Placenta
29	chr1:224687200-224690000	Weak transcription	Small Intestine	intestine
30	chr1:224687200-224690200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:224687200-224690400	Weak transcription	Fetal Kidney	kidney
32	chr1:224687200-224690600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:224687400-224690000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:224687400-224690000	Weak transcription	Brain Substantia Nigra	brain
35	chr1:224687400-224690200	Weak transcription	Hela-S3	cervix
36	chr1:224687400-224690400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:224687400-224690400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:224687400-224691000	Weak transcription	HSMMtube	muscle
39	chr1:224687600-224690000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:224687600-224690200	Weak transcription	NH-A	brain
41	chr1:224687800-224690000	Weak transcription	Brain Anterior Caudate	brain
42	chr1:224687800-224692600	Enhancers	Fetal Thymus	thymus
43	chr1:224688200-224690000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:224688200-224690000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:224688400-224690000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:224688400-224690400	Enhancers	K562	blood
47	chr1:224688600-224690000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:224688600-224690200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr1:224688600-224690200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:224688600-224694400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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