Variant report

Variant	rs4763879
Chromosome Location	chr12:9910164-9910165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:9907740..9910735-chr12:10101487..10103775,2	K562	blood:
2	chr12:9908727..9910946-chr12:9954413..9956000,2	K562	blood:
3	chr12:9514676..9517481-chr12:9908794..9910668,2	K562	blood:
4	chr12:9803491..9806822-chr12:9909601..9912697,3	K562	blood:
5	chr12:9909065..9911051-chr12:10072172..10073790,2	K562	blood:
6	chr12:9889267..9893240-chr12:9909352..9912451,4	K562	blood:
7	chr12:9909977..9913009-chr12:10364990..10367233,3	K562	blood:
8	chr12:9908521..9910612-chr12:10055343..10056923,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139112	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1008610	0.82[JPT][hapmap]
rs1044771	0.80[ASW][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap]
rs10492165	0.82[JPT][hapmap]
rs10492166	0.82[JPT][hapmap]
rs10772087	0.82[JPT][hapmap]
rs10772102	0.82[JPT][hapmap]
rs10844620	0.80[JPT][hapmap]
rs10844636	0.82[JPT][hapmap]
rs10844638	0.82[JPT][hapmap]
rs10844657	0.82[JPT][hapmap]
rs10844706	0.91[JPT][hapmap]
rs11052877	0.82[JPT][hapmap]
rs2098298	0.84[JPT][hapmap]
rs3136559	0.87[MKK][hapmap]
rs4763840	0.86[JPT][hapmap]
rs61163981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310460	0.80[ASW][hapmap]
rs917911	0.86[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9332411	0.80[ASW][hapmap]

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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv3431702	chr12:9910073-9910586	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 1 diabetes	19430480	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4763879	DCAL1	cis	multi-tissue	Pritchard
rs4763879	CLEC2D	cis	multi-tissue	Pritchard
rs4763879	FOXJ2	cis	parietal	SCAN
rs4763879	PHC1	cis	lymphoblastoid	seeQTL
rs4763879	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL
rs4763879	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs4763879	CLEC2B	cis	multi-tissue	Pritchard
rs4763879	CLEC2A	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9893400-9910800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:9896400-9911000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:9903400-9917600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:9903600-9911000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:9903800-9911200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:9904000-9910200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:9904200-9910800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:9904200-9911200	Weak transcription	Small Intestine	intestine
9	chr12:9904400-9913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:9904600-9913400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr12:9905600-9913400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:9905800-9910600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:9908200-9910200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:9908800-9910600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:9909000-9914800	Active TSS	Thymus	Thymus
16	chr12:9909200-9910600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr12:9909200-9911200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr12:9909400-9910600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:9909400-9911000	Active TSS	GM12878-XiMat	blood
20	chr12:9909600-9913400	Active TSS	Fetal Thymus	thymus
21	chr12:9909600-9914200	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr12:9909800-9910200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr12:9909800-9910200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr12:9909800-9910400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr12:9909800-9910600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr12:9909800-9910800	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:9909800-9910800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
28	chr12:9909800-9910800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:9909800-9911400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
30	chr12:9909800-9911400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:9909800-9914000	Active TSS	K562	blood
32	chr12:9909800-9914400	Active TSS	Primary T cells fromperipheralblood	blood
33	chr12:9910000-9910200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:9910000-9910200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:9910000-9910400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:9910000-9910400	Transcr. at gene 5' and 3'	Dnd41	blood

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