Variant report

Variant	rs9430244
Chromosome Location	chr1:10155283-10155284
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	chr1:10092400..10094364-chr1:10154481..10156990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11121515	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11121517	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121519	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12030552	0.82[AFR][1000 genomes]
rs12058944	0.83[YRI][hapmap]
rs12068865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12076005	0.83[YRI][hapmap]
rs12087114	0.86[ASW][hapmap]
rs74051808	0.98[ASN][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	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
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9430244	LZIC	cis	lymphoblastoid	seeQTL
rs9430244	APITD1	cis	parietal	SCAN
rs9430244	HES3	cis	cerebellum	SCAN
rs9430244	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs9430244	LZIC	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10106800-10155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:10109400-10158400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:10118200-10163000	Weak transcription	Aorta	Aorta
5	chr1:10120000-10156400	Weak transcription	Spleen	Spleen
6	chr1:10120000-10162600	Weak transcription	Gastric	stomach
7	chr1:10120400-10163000	Weak transcription	Fetal Kidney	kidney
8	chr1:10125800-10165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:10125800-10165400	Weak transcription	Fetal Brain Male	brain
10	chr1:10126000-10161000	Weak transcription	A549	lung
11	chr1:10126400-10162800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:10126400-10163000	Weak transcription	Pancreas	Pancrea
13	chr1:10126400-10165400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:10132200-10156000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:10132400-10155400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:10132400-10163000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:10132600-10162600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:10132600-10165400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:10134600-10166200	Weak transcription	Colonic Mucosa	Colon
20	chr1:10134600-10166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:10134800-10163000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:10135000-10160400	Weak transcription	Ovary	ovary
23	chr1:10135200-10155400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:10135200-10155400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:10135200-10164200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:10135200-10165400	Weak transcription	HUVEC	blood vessel
27	chr1:10135600-10162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:10135800-10161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:10135800-10164200	Weak transcription	NH-A	brain
30	chr1:10135800-10164200	Weak transcription	NHLF	lung
31	chr1:10136200-10155400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:10136200-10164000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:10137600-10165600	Weak transcription	Esophagus	oesophagus
34	chr1:10137800-10161200	Weak transcription	Osteobl	bone
35	chr1:10140800-10162800	Weak transcription	Brain Anterior Caudate	brain
36	chr1:10141000-10161000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:10141000-10164200	Weak transcription	Fetal Brain Female	brain
38	chr1:10141200-10158600	Weak transcription	Fetal Lung	lung
39	chr1:10142400-10161000	Weak transcription	Hela-S3	cervix
40	chr1:10142600-10155400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:10143600-10161000	Weak transcription	NHDF-Ad	bronchial
42	chr1:10143800-10158400	Weak transcription	HSMM	muscle
43	chr1:10144000-10155400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:10144000-10163000	Weak transcription	NHEK	skin
45	chr1:10144000-10165400	Weak transcription	HSMMtube	muscle
46	chr1:10144400-10155800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:10144400-10159800	Weak transcription	GM12878-XiMat	blood
48	chr1:10144400-10163000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:10144400-10164000	Weak transcription	Right Ventricle	heart
50	chr1:10144600-10160800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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