Variant report

Variant	rs6488176
Chromosome Location	chr12:9896333-9896334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9884042..9890048-chr12:9890384..9897967,9	K562	blood:
2	chr12:9894583..9897209-chr12:9902973..9905034,4	K562	blood:
3	chr12:9895231..9897767-chr12:9915766..9917544,2	K562	blood:

Variant related genes	Relation type
ENSG00000184293	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10161013	0.91[EUR][1000 genomes]
rs10743828	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772093	0.91[EUR][1000 genomes]
rs10772099	0.92[EUR][1000 genomes]
rs10772106	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10844656	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11835594	0.91[EUR][1000 genomes]
rs12304982	0.89[EUR][1000 genomes]
rs12820281	0.92[EUR][1000 genomes]
rs12824727	0.90[EUR][1000 genomes]
rs13377908	0.91[EUR][1000 genomes]
rs13377939	0.91[EUR][1000 genomes]
rs16927874	0.91[EUR][1000 genomes]
rs17806015	1.00[ASN][1000 genomes]
rs2268145	0.91[EUR][1000 genomes]
rs3136576	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176793	1.00[ASN][1000 genomes]
rs34584384	0.86[EUR][1000 genomes]
rs34633868	0.88[EUR][1000 genomes]
rs35990903	0.91[EUR][1000 genomes]
rs3922289	0.90[EUR][1000 genomes]
rs4763296	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4763299	1.00[ASN][1000 genomes]
rs4763864	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59016059	0.91[EUR][1000 genomes]
rs71447599	0.92[EUR][1000 genomes]
rs71447600	0.91[EUR][1000 genomes]
rs7301386	0.91[EUR][1000 genomes]
rs74062708	0.82[EUR][1000 genomes]
rs766502	1.00[ASN][1000 genomes]
rs7962964	0.90[EUR][1000 genomes]
rs7964917	0.91[EUR][1000 genomes]
rs7969022	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976474	0.91[EUR][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	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	nsv8911	chr12:9895900-9897691	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6488176	RP11-75L1.2	cis	Whole Blood	GTEx
rs6488176	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs6488176	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9890400-9897600	Weak transcription	HUVEC	blood vessel
2	chr12:9892800-9903200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:9893000-9896400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:9893000-9896800	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:9893400-9910800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:9894200-9896800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:9894800-9896400	Flanking Active TSS	GM12878-XiMat	blood
8	chr12:9895200-9896400	Enhancers	Duodenum Mucosa	Duodenum
9	chr12:9895400-9896600	Enhancers	Primary B cells from cord blood	blood
10	chr12:9895600-9896400	Enhancers	K562	blood
11	chr12:9895600-9896800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:9895600-9896800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:9895600-9897200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:9895600-9897200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:9895600-9897400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr12:9895600-9906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:9895800-9896600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:9895800-9896600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr12:9895800-9896800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:9895800-9896800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:9895800-9897200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:9895800-9897400	Enhancers	Primary T cells from cord blood	blood
23	chr12:9895800-9897400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:9895800-9898000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr12:9895800-9903200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:9896200-9896400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr12:9896200-9896800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:9896200-9896800	Bivalent Enhancer	Dnd41	blood
29	chr12:9896200-9903200	Weak transcription	Monocytes-CD14+_RO01746	blood

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