Variant report

Variant	rs1059612
Chromosome Location	chr6:30708955-30708956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr6:30707405-30712696	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:30708766-30709176	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr6:30704670-30712656	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:30708838-30712666	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr6:30708868-30712745	HCT-116	colon:	n/a	n/a
6	POLR2A	chr6:30707434-30712732	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr6:30707893-30713121	HepG2	liver:	n/a	n/a
8	RAD21	chr6:30708848-30709136	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr6:30708920-30709070	NHEK	skin:	n/a	n/a
10	POLR2A	chr6:30708940-30712572	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr6:30708940-30709090	GM12872	blood:	n/a	n/a
12	CTCF	chr6:30708920-30709070	AG09319	gingival:	n/a	n/a
13	POLR2A	chr6:30708868-30709244	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr6:30708846-30709167	HCT-116	colon:	n/a	n/a
15	CTCF	chr6:30708900-30709050	WERI-Rb-1	eye:	n/a	n/a
16	CHD1	chr6:30707429-30712681	IMR90	lung:	n/a	chr6:30710901-30710911 chr6:30710526-30710536
17	SIN3AK20	chr6:30708737-30709302	PANC-1	pancreas:	n/a	n/a
18	USF2	chr6:30708923-30708995	GM12878	blood:	n/a	n/a
19	CTCF	chr6:30708860-30709010	BJ	skin:	n/a	n/a
20	POLR2A	chr6:30707359-30712662	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr6:30708901-30708976	HepG2	liver:	n/a	n/a
22	CTCF	chr6:30708880-30709030	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:30708898-30709056	A549	lung:	n/a	n/a
24	CTCF	chr6:30708900-30709050	AG10803	skin:	n/a	n/a
25	CTCF	chr6:30708926-30709126	GM12878	blood:	n/a	n/a
26	CTCF	chr6:30708900-30709050	GM12875	blood:	n/a	n/a
27	RAD21	chr6:30708916-30709085	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr6:30708920-30709070	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr6:30704619-30712530	IMR90	lung:	n/a	n/a
30	POLR2A	chr6:30708847-30712517	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:30708852-30712554	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr6:30708789-30712673	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:30708787-30712678	K562	blood:	n/a	n/a
34	POLR2A	chr6:30707325-30712778	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr6:30708862-30711131	MCF-7	breast:	n/a	n/a
36	CTCF	chr6:30708900-30709050	AG04449	skin:	n/a	n/a
37	POLR2A	chr6:30708797-30709118	HepG2	liver:	n/a	n/a
38	POLR2A	chr6:30708886-30712616	PBDE	blood:	n/a	n/a
39	CTCF	chr6:30708900-30709050	HFF	foreskin:	n/a	n/a
40	CTCF	chr6:30708945-30709068	GM19238	blood:	n/a	n/a
41	POLR2A	chr6:30708741-30709192	MCF-7	breast:	n/a	n/a
42	HEY1	chr6:30707427-30712781	HepG2	liver:	n/a	chr6:30710563-30710578
43	POLR2A	chr6:30707409-30712524	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr6:30707894-30712665	U87	brain:	n/a	n/a
45	CTCF	chr6:30708880-30709030	Caco-2	colon:	n/a	n/a
46	POLR2A	chr6:30708696-30712691	GM12892	blood:	n/a	n/a
47	MAZ	chr6:30707288-30712786	IMR90	lung:	n/a	chr6:30710671-30710680
48	POLR2A	chr6:30707388-30712490	A549	lung:	n/a	n/a
49	POLR2A	chr6:30708948-30712615	U87	brain:	n/a	n/a
50	POLR2A	chr6:30707270-30712612	GM12878	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30523845..30525398-chr6:30708449..30710069,2	MCF-7	breast:
2	chr6:30707945..30712505-chr6:30840794..30847673,9	K562	blood:
3	chr6:30707658..30710015-chr8:144677120..144679649,2	MCF-7	breast:
4	chr1:117451768..117453895-chr6:30707960..30710700,2	MCF-7	breast:
5	chr6:30581322..30587794-chr6:30705649..30714068,32	K562	blood:
6	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
7	chr6:30639079..30642784-chr6:30705636..30712325,12	MCF-7	breast:
8	chr6:30708481..30709308-chr7:32930305..32931147,2	Hela-S3	cervix:
9	chr5:179050328..179050981-chr6:30708892..30709826,2	Hela-S3	cervix:
10	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
11	chr11:118788904..118790575-chr6:30707843..30710033,2	MCF-7	breast:
12	chr6:30578948..30585851-chr6:30707403..30713755,14	MCF-7	breast:
13	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
14	chr1:145381364..145383003-chr6:30708944..30710900,2	MCF-7	breast:
15	chr6:30580645..30587403-chr6:30708153..30714600,16	MCF-7	breast:
16	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
17	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
18	chr17:57918223..57923763-chr6:30707801..30713436,10	MCF-7	breast:
19	chr6:30537121..30539529-chr6:30708411..30710426,2	MCF-7	breast:
20	chr6:30708700..30710764-chr6:30734085..30735975,2	K562	blood:
21	chr15:60687645..60690491-chr6:30708468..30710482,2	MCF-7	breast:
22	chr17:57922134..57925818-chr6:30708673..30712845,6	MCF-7	breast:
23	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:
24	chr14:81685583..81687779-chr6:30708570..30711390,2	MCF-7	breast:
25	chr6:30651552..30657864-chr6:30708721..30713716,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272273	TF binding region
ENSG00000201988	TF binding region
FLOT1	TF binding region
ENSG00000228022	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000272715	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000186174	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000170852	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000104529	Chromatin interaction
ENSG00000182718	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000134247	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000264731	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1049633	0.90[AMR][1000 genomes]
rs1264308	0.90[AMR][1000 genomes]
rs1264325	0.90[AMR][1000 genomes]
rs1264347	0.90[AMR][1000 genomes]
rs1264351	1.00[AMR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs2263298	0.90[AMR][1000 genomes]
rs2517578	0.90[AMR][1000 genomes]
rs2524266	0.83[AMR][1000 genomes]
rs2535328	0.90[AMR][1000 genomes]
rs2535332	0.90[AMR][1000 genomes]
rs2535334	0.90[AMR][1000 genomes]
rs2535340	0.90[AMR][1000 genomes]
rs2844656	0.90[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes]
rs3094118	0.86[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3095327	0.91[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3095334	0.85[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3129977	0.83[EUR][1000 genomes]
rs3129978	0.85[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130665	0.86[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130673	0.85[EUR][1000 genomes]
rs3131041	0.80[EUR][1000 genomes]
rs3131052	0.80[EUR][1000 genomes]
rs3132577	0.90[AMR][1000 genomes]
rs3132582	0.91[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132599	0.85[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132603	0.85[EUR][1000 genomes]
rs3132605	0.85[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes]
rs886422	0.90[AMR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9262143	0.93[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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 miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
10	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1059612	HIST1H2BM	cis	cerebellum	SCAN
rs1059612	ZNF323	cis	parietal	SCAN
rs1059612	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:30693400-30709000	Strong transcription	Fetal Stomach	stomach
4	chr6:30693800-30709000	Strong transcription	Fetal Brain Female	brain
5	chr6:30695400-30709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:30695400-30709200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:30696400-30709000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:30697000-30709200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:30698800-30709000	Strong transcription	Fetal Intestine Large	intestine
10	chr6:30698800-30709200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:30700600-30709200	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr6:30702400-30709200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr6:30703400-30709200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:30703600-30709000	Genic enhancers	Adipose Nuclei	Adipose
15	chr6:30704800-30709200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:30705000-30709000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:30705200-30709000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:30705200-30709000	Strong transcription	Fetal Kidney	kidney
19	chr6:30705200-30709000	Genic enhancers	K562	blood
20	chr6:30705400-30709200	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr6:30705400-30709400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:30705400-30709600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:30705600-30709000	Genic enhancers	A549	lung
24	chr6:30705800-30709000	Strong transcription	Fetal Lung	lung
25	chr6:30705800-30709200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30705800-30709200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:30705800-30709400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:30706000-30709000	Weak transcription	Small Intestine	intestine
29	chr6:30706000-30709200	Genic enhancers	HUVEC	blood vessel
30	chr6:30706400-30709000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:30706600-30709000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:30706600-30709000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:30706600-30709000	Strong transcription	Esophagus	oesophagus
34	chr6:30706800-30709000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:30706800-30709000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:30706800-30709000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:30706800-30709200	Weak transcription	Psoas Muscle	Psoas
38	chr6:30707000-30709400	Genic enhancers	Placenta	Placenta
39	chr6:30707400-30709200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:30707400-30709200	Genic enhancers	NHDF-Ad	bronchial
41	chr6:30707400-30709400	Genic enhancers	Pancreas	Pancrea
42	chr6:30707600-30709000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:30707600-30709000	Genic enhancers	Osteobl	bone
44	chr6:30707600-30709200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:30707600-30709200	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr6:30707800-30709000	Genic enhancers	Colon Smooth Muscle	Colon
47	chr6:30707800-30709000	Genic enhancers	Rectal Smooth Muscle	rectum
48	chr6:30707800-30709000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr6:30707800-30709000	Genic enhancers	GM12878-XiMat	blood
50	chr6:30707800-30709000	Enhancers	NH-A	brain

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