Variant report

Variant	rs3130968
Chromosome Location	chr6:31065071-31065072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30710595..30712129-chr6:31063748..31065436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2517546	0.81[EUR][1000 genomes]
rs2535296	0.84[EUR][1000 genomes]
rs3094087	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094671	0.82[EUR][1000 genomes]
rs3095311	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130968	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31058800-31066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:31060600-31065200	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:31060800-31066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:31061000-31065800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:31061600-31065600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:31061600-31065600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:31061800-31066000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:31062000-31065200	Enhancers	Spleen	Spleen
9	chr6:31062600-31065800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:31062600-31066600	Enhancers	HUVEC	blood vessel
11	chr6:31062800-31065400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:31062800-31065600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr6:31062800-31065800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:31062800-31066000	Weak transcription	Lung	lung
15	chr6:31062800-31070000	Weak transcription	A549	lung
16	chr6:31063000-31065800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:31063000-31065800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:31063000-31065800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:31063200-31065600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:31063200-31065600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:31063200-31070000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:31063200-31070000	Weak transcription	HMEC	breast
23	chr6:31064600-31065400	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:31064600-31065600	Enhancers	HepG2	liver
25	chr6:31064800-31065600	Enhancers	Primary T cells from cord blood	blood
26	chr6:31064800-31066200	Enhancers	K562	blood
27	chr6:31065000-31066800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:31065000-31077600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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