Variant report

Variant	rs9391630
Chromosome Location	chr6:29722515-29722516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29710119..29712623-chr6:29721345..29723379,2	MCF-7	breast:
2	chr6:29721433..29724421-chr6:29794290..29797232,2	MCF-7	breast:
3	chr6:29721629..29723965-chr6:29782354..29784325,2	K562	blood:

Variant related genes	Relation type
ENSG00000204632	Chromatin interaction
ENSG00000229142	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12661228	0.82[EUR][1000 genomes]
rs12661266	0.82[EUR][1000 genomes]
rs16867712	0.92[EUR][1000 genomes]
rs17184549	0.82[EUR][1000 genomes]
rs17875376	0.85[EUR][1000 genomes]
rs2394164	0.86[EUR][1000 genomes]
rs34260811	0.90[EUR][1000 genomes]
rs34387568	0.82[EUR][1000 genomes]
rs34912326	0.82[EUR][1000 genomes]
rs35471702	0.83[EUR][1000 genomes]
rs4084764	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4391284	0.80[EUR][1000 genomes]
rs4713233	0.80[EUR][1000 genomes]
rs4713237	0.87[EUR][1000 genomes]
rs4713239	0.88[EUR][1000 genomes]
rs4713240	0.88[EUR][1000 genomes]
rs4713242	0.84[EUR][1000 genomes]
rs4713244	0.91[EUR][1000 genomes]
rs7754067	0.91[EUR][1000 genomes]
rs7759474	0.91[EUR][1000 genomes]
rs7759482	0.91[EUR][1000 genomes]
rs9368609	0.89[EUR][1000 genomes]
rs9391660	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9391630	HMGN4	cis	cerebellum	SCAN
rs9391630	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9391630	ZKSCAN3	cis	cerebellum	SCAN
rs9391630	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29721000-29723000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:29721000-29723200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29721000-29723200	Weak transcription	Spleen	Spleen
4	chr6:29721000-29724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:29721000-29725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:29721200-29723200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:29721200-29723200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:29721200-29723200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:29721200-29723600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:29721400-29723000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:29721400-29724600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:29721600-29723000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:29721600-29723000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:29721600-29724600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:29721600-29725400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:29721600-29729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:29721800-29723000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:29721800-29723800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:29721800-29724600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:29721800-29725400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:29721800-29725400	Weak transcription	Hela-S3	cervix
22	chr6:29721800-29725400	Weak transcription	HMEC	breast

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