Variant report

Variant	rs3814959
Chromosome Location	chr6:30594827-30594828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr6:30594526-30594927	GM12878	blood:	n/a	n/a
2	MAX	chr6:30594346-30594867	A549	lung:	n/a	chr6:30594436-30594445
3	MYC	chr6:30594434-30594840	MCF-7	breast:	n/a	chr6:30594436-30594445
4	TCF7L2	chr6:30594416-30595088	HCT-116	colon:	n/a	n/a
5	CREB1	chr6:30594386-30594974	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr6:30594308-30594894	GM12891	blood:	n/a	n/a
7	TAF1	chr6:30594428-30594889	HepG2	liver:	n/a	n/a
8	MAX	chr6:30594257-30595005	ECC-1	luminal epithelium:	n/a	chr6:30594436-30594445
9	STAT5A	chr6:30594338-30595161	GM12878	blood:	n/a	chr6:30594575-30594582
10	POLR2A	chr6:30594015-30595207	K562	blood:	n/a	n/a
11	SP4	chr6:30594359-30594850	H1-hESC	embryonic stem cell:	n/a	chr6:30594830-30594846 chr6:30594606-30594617 chr6:30594591-30594602 chr6:30594832-30594848
12	CHD1	chr6:30594480-30594994	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:30593969-30594981	PANC-1	pancreas:	n/a	n/a
14	SPI1	chr6:30594282-30595106	GM12878	blood:	n/a	n/a
15	MTA3	chr6:30594134-30595237	GM12878	blood:	n/a	n/a
16	ZBTB33	chr6:30594307-30594838	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:30594285-30594913	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:30594431-30594899	HEK293	kidney:	n/a	n/a
19	FOSL2	chr6:30594221-30594916	HepG2	liver:	n/a	n/a
20	TCF7L2	chr6:30594446-30595147	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr6:30593561-30595349	K562	blood:	n/a	n/a
22	POLR2A	chr6:30594277-30594879	A549	lung:	n/a	n/a
23	NR2C2	chr6:30594467-30595136	GM12878	blood:	n/a	chr6:30594942-30594955 chr6:30594895-30594908 chr6:30594897-30594906 chr6:30594944-30594953
24	PBX3	chr6:30594294-30594924	A549	lung:	n/a	n/a
25	POLR2A	chr6:30594195-30595206	GM12878	blood:	n/a	n/a
26	CREB1	chr6:30594399-30594840	ECC-1	luminal epithelium:	n/a	n/a
27	ELF1	chr6:30594427-30595018	HepG2	liver:	n/a	chr6:30594611-30594624
28	MAX	chr6:30594394-30594886	HepG2	liver:	n/a	chr6:30594436-30594445
29	CREB1	chr6:30594310-30595171	HepG2	liver:	n/a	n/a
30	MBD4	chr6:30594064-30595056	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:30594125-30595079	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr6:30594209-30594962	GM12892	blood:	n/a	n/a
33	NR2C2	chr6:30594479-30595143	HepG2	liver:	n/a	chr6:30594942-30594955 chr6:30594895-30594908 chr6:30594897-30594906 chr6:30594944-30594953
34	MAZ	chr6:30594402-30594862	GM12878	blood:	n/a	chr6:30594436-30594445
35	REST	chr6:30593978-30595485	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr6:30594330-30594920	GM19193	blood:	n/a	n/a
37	POLR2A	chr6:30594140-30595048	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:30593812-30595222	PFSK-1	brain:	n/a	n/a
39	NFIC	chr6:30594313-30594989	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:30594507-30594883	H1-hESC	embryonic stem cell:	n/a	n/a
41	SIN3AK20	chr6:30594352-30594917	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:30594143-30594976	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:30594243-30594903	K562	blood:	n/a	n/a
44	TCF12	chr6:30594065-30594988	A549	lung:	n/a	n/a
45	POLR2A	chr6:30594258-30594908	HepG2	liver:	n/a	n/a
46	JUND	chr6:30594354-30594945	HepG2	liver:	n/a	n/a
47	TBL1XR1	chr6:30594468-30594967	GM12878	blood:	n/a	n/a
48	EP300	chr6:30594437-30594885	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:30594337-30594921	Gliobla	brain:	n/a	n/a
50	HMGN3	chr6:30594323-30594879	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30592745..30596299-chr6:30612825..30617200,8	MCF-7	breast:
2	chr6:30593365..30595936-chr6:30888888..30891859,2	K562	blood:
3	chr6:30594510..30596301-chr6:30639461..30642198,2	MCF-7	breast:
4	chr6:30593119..30595589-chr6:30619964..30621770,2	MCF-7	breast:
5	chr6:30523568..30525736-chr6:30593278..30596077,2	MCF-7	breast:
6	chr6:30591157..30598732-chr6:30607879..30619621,21	K562	blood:
7	chr6:30590782..30598373-chr6:30685661..30690473,13	MCF-7	breast:
8	chr6:30594160..30596394-chr6:30709286..30711112,2	MCF-7	breast:
9	chr6:30591444..30595401-chr6:30685466..30689259,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS18B-1	chr6:30594469-30594973	NONHSAT108654

Variant related genes	Relation type
ATAT1	TF binding region
ENSG00000204560	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000196230	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17189246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17189399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2239887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2269708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2301277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57302671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60447066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30593600-30613800	Weak transcription	Hela-S3	cervix
2	chr6:30594000-30595200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr6:30594000-30595200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:30594000-30595600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:30594200-30595000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:30594200-30595000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:30594200-30595000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:30594200-30595000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:30594200-30595000	Active TSS	Fetal Kidney	kidney
10	chr6:30594200-30595000	Flanking Active TSS	Pancreas	Pancrea
11	chr6:30594200-30595200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:30594200-30595200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr6:30594200-30595200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:30594200-30595200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr6:30594200-30595200	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr6:30594200-30595200	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr6:30594200-30595400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:30594200-30595400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr6:30594200-30595400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:30594200-30595400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr6:30594200-30595400	Active TSS	Right Ventricle	heart
22	chr6:30594200-30595400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:30594200-30595600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:30594200-30595600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:30594200-30595600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr6:30594200-30595600	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr6:30594200-30595600	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr6:30594200-30595600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr6:30594200-30595600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:30594200-30595600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr6:30594200-30596000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:30594200-30596000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:30594400-30595000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:30594400-30595000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:30594400-30595000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:30594400-30595000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30594400-30595000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:30594400-30595000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:30594400-30595000	Active TSS	Aorta	Aorta
40	chr6:30594400-30595000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:30594400-30595000	Active TSS	Colon Smooth Muscle	Colon
42	chr6:30594400-30595000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:30594400-30595000	Active TSS	Right Atrium	heart
44	chr6:30594400-30595000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr6:30594400-30595000	Active TSS	NHLF	lung
46	chr6:30594400-30595200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:30594400-30595200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr6:30594400-30595200	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr6:30594400-30595200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr6:30594400-30595200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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