Variant report

Variant	rs61785621
Chromosome Location	chr1:10009138-10009139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10008573..10013502-chr1:10090291..10096219,9	MCF-7	breast:
2	chr1:10006856..10008883-chr1:10008961..10010620,2	K562	blood:
3	chr1:10008967..10010504-chr1:10091583..10094511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202415	Chromatin interaction
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10779735	0.86[AFR][1000 genomes]
rs11121508	0.93[AFR][1000 genomes]
rs12128632	0.91[AFR][1000 genomes]
rs12128636	0.83[AFR][1000 genomes]
rs1220398	0.84[AFR][1000 genomes]
rs1220422	0.95[AFR][1000 genomes]
rs1237370	0.88[AFR][1000 genomes]
rs12744387	0.90[AFR][1000 genomes]
rs2380188	0.95[AFR][1000 genomes]
rs3013785	0.83[AFR][1000 genomes]
rs4073852	0.92[AFR][1000 genomes]
rs6541074	0.95[AFR][1000 genomes]
rs6663108	0.85[AFR][1000 genomes]
rs6673580	0.95[AFR][1000 genomes]
rs6683452	0.93[AFR][1000 genomes]
rs7522568	0.94[AFR][1000 genomes]
rs7534615	0.95[AFR][1000 genomes]
rs9943169	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61785621	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
3	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
4	chr1:10004200-10010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
6	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
8	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
9	chr1:10004200-10010600	Weak transcription	Ovary	ovary
10	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:10004200-10019400	Weak transcription	NH-A	brain
12	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:10004200-10033800	Weak transcription	Gastric	stomach
14	chr1:10004400-10009200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:10004400-10010000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:10004400-10010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:10004400-10010000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:10004400-10010000	Weak transcription	Stomach Mucosa	stomach
19	chr1:10004400-10010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:10004400-10010200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:10004400-10010200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:10004400-10010200	Weak transcription	Placenta	Placenta
23	chr1:10004400-10010400	Weak transcription	Esophagus	oesophagus
24	chr1:10004400-10010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:10004400-10010600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:10004400-10010600	Weak transcription	Fetal Brain Female	brain
27	chr1:10004400-10010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:10004400-10010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:10004400-10018200	Weak transcription	NHLF	lung
30	chr1:10004400-10021200	Weak transcription	HSMM	muscle
31	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
32	chr1:10004600-10009400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:10004600-10009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:10004600-10010400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:10004600-10010400	Weak transcription	Thymus	Thymus
36	chr1:10004600-10010600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:10004600-10010600	Weak transcription	NHDF-Ad	bronchial
38	chr1:10004600-10010600	Weak transcription	Osteobl	bone
39	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
40	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:10004800-10009800	Weak transcription	Brain Substantia Nigra	brain
42	chr1:10004800-10009800	Weak transcription	GM12878-XiMat	blood
43	chr1:10004800-10010000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:10004800-10010000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:10004800-10010000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:10004800-10010000	Weak transcription	Brain Anterior Caudate	brain
47	chr1:10004800-10010200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr1:10004800-10010200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:10004800-10010200	Weak transcription	Left Ventricle	heart
50	chr1:10004800-10010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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