Variant report

Variant	rs2230318
Chromosome Location	chr12:8211256-8211257
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	chr12:8185362..8188149-chr12:8209815..8211810,2	K562	blood:
2	chr12:8209418..8211639-chr12:8218119..8220540,2	K562	blood:

Variant related genes	Relation type
ENSG00000065970	Chromatin interaction
ENSG00000171860	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11567805	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3759280	1.00[GIH][hapmap]
rs3782678	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
13	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2230318	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8192600-8212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:8201000-8211600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:8203000-8218800	Weak transcription	HMEC	breast
4	chr12:8203400-8217400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:8205600-8211400	Weak transcription	HUVEC	blood vessel
6	chr12:8205600-8212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:8205600-8214200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:8205600-8218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:8205600-8218800	Weak transcription	Hela-S3	cervix
10	chr12:8206000-8214000	Weak transcription	Pancreas	Pancrea
11	chr12:8206000-8221600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:8206200-8217200	Weak transcription	K562	blood
13	chr12:8206200-8218800	Weak transcription	NH-A	brain
14	chr12:8206600-8212200	Weak transcription	Spleen	Spleen
15	chr12:8206600-8216800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:8206800-8218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:8207600-8211400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:8207600-8215400	Weak transcription	Colonic Mucosa	Colon
19	chr12:8207600-8217200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:8207600-8217800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:8207600-8218800	Weak transcription	NHDF-Ad	bronchial
22	chr12:8207800-8212200	Weak transcription	Lung	lung
23	chr12:8207800-8217000	Weak transcription	Placenta	Placenta
24	chr12:8207800-8218000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:8207800-8218400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:8207800-8221400	Weak transcription	Brain Substantia Nigra	brain
27	chr12:8208000-8212200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:8208000-8214000	Weak transcription	Gastric	stomach
29	chr12:8208000-8217400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:8208000-8217400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:8208000-8218400	Weak transcription	GM12878-XiMat	blood
32	chr12:8208000-8218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:8208000-8218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:8208000-8218800	Weak transcription	Thymus	Thymus
35	chr12:8208200-8216400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr12:8208200-8218400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:8208200-8218800	Weak transcription	Fetal Thymus	thymus
38	chr12:8208400-8211400	Weak transcription	Brain Anterior Caudate	brain
39	chr12:8208400-8211400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:8208400-8212200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:8208400-8212200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:8208400-8214000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:8208400-8216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:8208400-8216600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:8208400-8216800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:8208400-8217400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:8208400-8217400	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:8208400-8217400	Weak transcription	Left Ventricle	heart
49	chr12:8208400-8217600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:8208400-8218200	Weak transcription	Dnd41	blood

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