Variant report

Variant	rs12068865
Chromosome Location	chr1:10141346-10141347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10864441	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11121515	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11121517	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11121519	0.87[ASN][1000 genomes]
rs12030552	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564842	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74051808	1.00[ASN][1000 genomes]
rs9430244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12068865	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:10106800-10155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:10109400-10158400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:10116600-10145000	Weak transcription	Stomach Mucosa	stomach
6	chr1:10118200-10163000	Weak transcription	Aorta	Aorta
7	chr1:10119200-10155200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:10120000-10156400	Weak transcription	Spleen	Spleen
9	chr1:10120000-10162600	Weak transcription	Gastric	stomach
10	chr1:10120400-10163000	Weak transcription	Fetal Kidney	kidney
11	chr1:10121800-10141400	Weak transcription	Hela-S3	cervix
12	chr1:10124400-10155200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:10125800-10165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:10125800-10165400	Weak transcription	Fetal Brain Male	brain
15	chr1:10126000-10154800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:10126000-10161000	Weak transcription	A549	lung
17	chr1:10126400-10162800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:10126400-10163000	Weak transcription	Pancreas	Pancrea
19	chr1:10126400-10165400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:10128000-10144800	Weak transcription	Psoas Muscle	Psoas
21	chr1:10129000-10145200	Weak transcription	Right Atrium	heart
22	chr1:10132200-10145000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:10132200-10156000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:10132400-10155200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:10132400-10155400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:10132400-10163000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:10132600-10162600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:10132600-10165400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:10134600-10166200	Weak transcription	Colonic Mucosa	Colon
30	chr1:10134600-10166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:10134800-10141600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:10134800-10163000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:10135000-10143400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:10135000-10154800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:10135000-10160400	Weak transcription	Ovary	ovary
36	chr1:10135200-10143600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:10135200-10155400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:10135200-10155400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:10135200-10164200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:10135200-10165400	Weak transcription	HUVEC	blood vessel
41	chr1:10135400-10144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:10135600-10143000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:10135600-10143200	Weak transcription	HSMM	muscle
44	chr1:10135600-10143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:10135600-10143800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:10135600-10144200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:10135600-10149800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:10135600-10155000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:10135600-10162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:10135800-10142200	Weak transcription	HMEC	breast

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