Variant report

Variant	rs56115353
Chromosome Location	chr6:12008085-12008086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr6:12008006-12009276	HEK293	kidney:	n/a	chr6:12008919-12008933
2	POLR2A	chr6:12007817-12015834	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:12007783-12012797	K562	blood:	n/a	n/a
4	POLR2A	chr6:12008070-12008464	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:12007820-12009828	K562	blood:	n/a	n/a
6	POLR2A	chr6:12007701-12009371	GM12891	blood:	n/a	n/a
7	JUN	chr6:12008032-12009732	K562	blood:	n/a	n/a
8	POLR2A	chr6:12007858-12013838	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:12007769-12009891	K562	blood:	n/a	n/a
10	POLR2A	chr6:12007639-12012082	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:12007795-12008291	K562	blood:	n/a	n/a
12	POLR2A	chr6:12007582-12014072	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:12007665-12011477	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:12007700-12012763	K562	blood:	n/a	n/a
15	ARID3A	chr6:12007786-12008220	HepG2	liver:	n/a	n/a
16	FOXA1	chr6:12007949-12008322	T-47D	breast:	n/a	n/a
17	POLR2A	chr6:12007727-12013607	K562	blood:	n/a	n/a
18	NFATC1	chr6:12008074-12011865	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:12007806-12011601	GM12891	blood:	n/a	n/a
20	POLR2A	chr6:12007580-12016124	GM12878	blood:	n/a	n/a
21	ARID3A	chr6:12007783-12009305	K562	blood:	n/a	n/a
22	POLR2A	chr6:12007705-12009372	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:12007620-12009364	GM12891	blood:	n/a	n/a
24	UBTF	chr6:12007884-12013591	K562	blood:	n/a	n/a
25	GATA3	chr6:12007951-12008358	T-47D	breast:	n/a	n/a
26	HEY1	chr6:12007751-12008103	K562	blood:	n/a	n/a
27	TBP	chr6:12007749-12009849	K562	blood:	n/a	n/a
28	MXI1	chr6:12007801-12010187	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr6:12007635-12013762	K562	blood:	n/a	n/a
30	GATA3	chr6:12007923-12008324	T-47D	breast:	n/a	n/a
31	POLR2A	chr6:12007804-12010285	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:12007733-12009305	GM12891	blood:	n/a	n/a
33	POLR2A	chr6:12007581-12012142	GM12892	blood:	n/a	n/a
34	MYC	chr6:12007786-12012740	K562	blood:	n/a	chr6:12009161-12009170
35	JUND	chr6:12007784-12009823	K562	blood:	n/a	n/a
36	MTA3	chr6:12007768-12009358	GM12878	blood:	n/a	n/a
37	GATA1	chr6:12008073-12009627	PBDE	blood:	n/a	n/a
38	FOXA1	chr6:12007988-12008265	T-47D	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11990947..11994181-chr6:12007149..12010077,3	K562	blood:
2	chr6:11733150..11736062-chr6:12007778..12010289,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf105-5	chr6:12007817-12008266	NONHSAT107775

No data

Variant related genes	Relation type
ENSG00000229896	TF binding region
HIVEP1	TF binding region
ENSG00000225102	Chromatin interaction
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs16872190	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486670	1.00[AFR][1000 genomes]
rs17486782	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17676319	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2024579	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41273100	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698720	1.00[ASN][1000 genomes]
rs55706944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55718735	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55760539	1.00[ASN][1000 genomes]
rs55797398	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55819840	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55839618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55875423	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55911725	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55964029	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56050214	1.00[ASN][1000 genomes]
rs56087670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204496	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56209525	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294425	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321224	1.00[ASN][1000 genomes]
rs56412238	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56764416	1.00[ASN][1000 genomes]
rs57774273	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58026118	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58086722	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58221347	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58831065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59206097	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59592071	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60200272	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60552066	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61227873	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62395405	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6458056	1.00[ASN][1000 genomes]
rs66530314	1.00[ASN][1000 genomes]
rs66614912	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66708680	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66720565	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66727286	1.00[ASN][1000 genomes]
rs66964129	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67170588	1.00[ASN][1000 genomes]
rs67757013	1.00[ASN][1000 genomes]
rs67843209	1.00[ASN][1000 genomes]
rs68009879	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68019130	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6916070	1.00[ASN][1000 genomes]
rs72826009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826025	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826027	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826092	1.00[ASN][1000 genomes]
rs72828105	1.00[ASN][1000 genomes]
rs742750	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs876829	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv970323	chr6:12006884-12020375	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv10446	chr6:12008060-12013799	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11999600-12008400	Weak transcription	Psoas Muscle	Psoas
2	chr6:12001600-12008400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:12001800-12008200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:12001800-12008400	Weak transcription	Osteobl	bone
5	chr6:12002000-12008200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:12002000-12008200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:12002200-12008400	Weak transcription	Adipose Nuclei	Adipose
8	chr6:12002200-12008400	Weak transcription	Fetal Brain Female	brain
9	chr6:12007000-12008200	Enhancers	Fetal Intestine Large	intestine
10	chr6:12007200-12008200	Enhancers	Fetal Heart	heart
11	chr6:12007200-12008200	Enhancers	Fetal Intestine Small	intestine
12	chr6:12007200-12008200	Enhancers	Fetal Lung	lung
13	chr6:12007200-12008600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:12007400-12008200	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:12007400-12008200	Enhancers	Fetal Stomach	stomach
16	chr6:12007400-12008200	Enhancers	Pancreas	Pancrea
17	chr6:12007400-12008200	Weak transcription	NHDF-Ad	bronchial
18	chr6:12007400-12013400	Active TSS	K562	blood
19	chr6:12007600-12008400	Enhancers	Fetal Thymus	thymus
20	chr6:12007600-12008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:12007800-12008200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:12007800-12008200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:12007800-12008200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:12007800-12008200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:12007800-12008200	Enhancers	Primary T cells from cord blood	blood
26	chr6:12007800-12008200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr6:12007800-12008200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:12007800-12008200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:12007800-12008200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:12007800-12008200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:12007800-12008200	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr6:12007800-12008200	Enhancers	HMEC	breast
33	chr6:12007800-12008400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:12007800-12008400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:12007800-12008400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
36	chr6:12007800-12008400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:12007800-12008400	Flanking Active TSS	Fetal Kidney	kidney
38	chr6:12007800-12008400	Weak transcription	Lung	lung
39	chr6:12007800-12008400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr6:12007800-12008400	Enhancers	Rectal Smooth Muscle	rectum
41	chr6:12007800-12008600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:12007800-12008600	Enhancers	Small Intestine	intestine
43	chr6:12007800-12008800	Flanking Active TSS	Hela-S3	cervix
44	chr6:12007800-12008800	Flanking Active TSS	NHEK	skin
45	chr6:12007800-12009800	Active TSS	Liver	Liver
46	chr6:12007800-12009800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:12007800-12009800	Bivalent/Poised TSS	HepG2	liver
48	chr6:12007800-12011400	Active TSS	Fetal Muscle Trunk	muscle
49	chr6:12008000-12008200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr6:12008000-12008200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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