Variant report

Variant	rs12568108
Chromosome Location	chr1:225973777-225973778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225966963..225971678-chr1:225973611..225976928,7	K562	blood:
2	chr1:225963461..225967975-chr1:225968057..225975345,14	MCF-7	breast:
3	chr1:225972838..225977175-chr1:225978955..225982654,5	K562	blood:
4	chr1:225972604..225974913-chr1:226031852..226034952,4	K562	blood:

Variant related genes	Relation type
ENSG00000242861	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11583055	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs11587295	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11587753	1.00[AFR][1000 genomes]
rs11588167	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11588197	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11588766	1.00[AFR][1000 genomes]
rs3738045	1.00[AFR][1000 genomes]
rs3753658	1.00[ASW][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes]
rs3753659	1.00[AFR][1000 genomes]
rs3753660	1.00[AFR][1000 genomes]
rs4149222	1.00[AFR][1000 genomes]
rs45607741	1.00[AFR][1000 genomes]
rs56187333	1.00[AFR][1000 genomes]
rs61837988	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61837989	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61837991	1.00[AFR][1000 genomes]
rs61837993	1.00[AFR][1000 genomes]
rs61837995	1.00[AFR][1000 genomes]
rs61837996	1.00[AFR][1000 genomes];0.86[EUR][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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12568108	HLX	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225966800-225978600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:225967200-225978400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:225967800-225980200	Weak transcription	Stomach Mucosa	stomach
4	chr1:225968200-225980000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:225968600-225978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:225968800-225976200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:225968800-225976800	Strong transcription	NHEK	skin
8	chr1:225969000-225977200	Strong transcription	HMEC	breast
9	chr1:225969400-225976000	Weak transcription	Small Intestine	intestine
10	chr1:225969800-225976800	Strong transcription	Fetal Intestine Large	intestine
11	chr1:225969800-225983000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:225970000-225978400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:225970200-225976000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:225970200-225978600	Strong transcription	Fetal Thymus	thymus
15	chr1:225970200-225979800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:225970200-225983200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:225970400-225977200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:225970600-225974200	Weak transcription	Fetal Heart	heart
19	chr1:225970600-225977400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:225970600-225978400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:225970600-225978400	Strong transcription	Dnd41	blood
22	chr1:225970600-225980000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:225970600-225980600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:225970600-225981800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:225970800-225973800	Weak transcription	Fetal Brain Male	brain
26	chr1:225970800-225974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:225970800-225976000	Strong transcription	Hela-S3	cervix
28	chr1:225970800-225977200	Strong transcription	K562	blood
29	chr1:225970800-225977400	Strong transcription	Liver	Liver
30	chr1:225970800-225978400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:225970800-225982200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:225971000-225976800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:225971000-225979200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:225971000-225979200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:225971200-225977200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:225971200-225978600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:225971200-225978800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:225971200-225979600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:225971200-225979800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:225971200-225980000	Strong transcription	NH-A	brain
41	chr1:225971200-225980000	Strong transcription	Osteobl	bone
42	chr1:225971400-225976800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:225971400-225977200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:225971400-225977400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:225971400-225978400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:225971400-225978600	Strong transcription	Placenta	Placenta
47	chr1:225971400-225980000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:225971600-225973800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:225971600-225976400	Strong transcription	Ovary	ovary
50	chr1:225971600-225976800	Strong transcription	Primary T cells from cord blood	blood

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