Variant report

Variant	rs4946371
Chromosome Location	chr6:119256648-119256649
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	POLR2A	chr6:119255359-119256710	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:119255530-119256664	GM19193	blood:	n/a	n/a
3	MAZ	chr6:119255108-119256825	IMR90	lung:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
4	TRIM28	chr6:119255785-119256712	K562	blood:	n/a	n/a
5	TCF7L2	chr6:119255792-119256653	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr6:119255525-119256666	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr6:119255637-119256658	HUVEC	blood vessel:	n/a	n/a
8	NR2F2	chr6:119255605-119256835	K562	blood:	n/a	n/a
9	PML	chr6:119255563-119256669	K562	blood:	n/a	n/a
10	TEAD4	chr6:119255432-119256697	K562	blood:	n/a	n/a
11	SIN3AK20	chr6:119255468-119256686	MCF-7	breast:	n/a	n/a
12	IRF1	chr6:119255708-119256684	K562	blood:	n/a	chr6:119256399-119256413
13	POLR2A	chr6:119255452-119256707	GM18505	blood:	n/a	n/a
14	POLR2A	chr6:119255561-119256673	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr6:119255394-119256658	K562	blood:	n/a	n/a
16	POLR2A	chr6:119255530-119256777	U87	brain:	n/a	n/a
17	EP300	chr6:119255771-119256703	K562	blood:	n/a	chr6:119256199-119256215
18	MAZ	chr6:119255415-119256719	GM12878	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
19	MYBL2	chr6:119255629-119256821	HepG2	liver:	n/a	n/a
20	RCOR1	chr6:119255414-119256662	Hela-S3	cervix:	n/a	n/a
21	MYBL2	chr6:119255554-119256742	HepG2	liver:	n/a	n/a
22	TAF1	chr6:119255927-119256648	H1-hESC	embryonic stem cell:	n/a	n/a
23	NRF1	chr6:119255650-119256719	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr6:119255447-119256660	GM19099	blood:	n/a	n/a
25	POLR2A	chr6:119255592-119256656	K562	blood:	n/a	n/a
26	HEY1	chr6:119255550-119256648	K562	blood:	n/a	n/a
27	POLR2A	chr6:119255451-119256652	Raji	blood:	n/a	n/a
28	POLR2A	chr6:119255643-119256834	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr6:119256108-119256682	SK-N-SH	brain:	n/a	n/a
30	MXI1	chr6:119255355-119256679	IMR90	lung:	n/a	n/a
31	POLR2A	chr6:119255463-119256652	GM12892	blood:	n/a	n/a
32	POLR2A	chr6:119255545-119256687	H1-hESC	embryonic stem cell:	n/a	n/a
33	TCF12	chr6:119255540-119256680	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:119255235-119256683	H1-hESC	embryonic stem cell:	n/a	n/a
35	TBP	chr6:119256480-119256674	Hela-S3	cervix:	n/a	n/a
36	GTF2F1	chr6:119255745-119256721	K562	blood:	n/a	n/a
37	MXI1	chr6:119255522-119256718	HepG2	liver:	n/a	n/a
38	HA-E2F1	chr6:119255345-119256700	MCF-7	breast:	n/a	chr6:119255765-119255774 chr6:119255766-119255773 chr6:119255754-119255763 chr6:119255766-119255773 chr6:119255755-119255769 chr6:119255797-119255807 chr6:119255766-119255773
39	TBL1XR1	chr6:119256296-119256743	K562	blood:	n/a	n/a
40	TEAD4	chr6:119255668-119256701	K562	blood:	n/a	n/a
41	POLR2A	chr6:119255537-119256668	K562	blood:	n/a	n/a
42	POLR2A	chr6:119255595-119256929	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr6:119255505-119256653	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:119255468-119256673	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr6:119255492-119256777	U87	brain:	n/a	n/a
46	POLR2A	chr6:119255468-119256689	K562	blood:	n/a	n/a
47	EP300	chr6:119255911-119256651	GM12878	blood:	n/a	chr6:119256199-119256215
48	POLR2A	chr6:119255546-119256659	GM18526	blood:	n/a	n/a
49	ELF1	chr6:119255999-119256677	MCF-7	breast:	n/a	chr6:119256313-119256326
50	HEY1	chr6:119255438-119256687	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
2	chr4:79472622..79473237-chr6:119256049..119256758,2	HCT-116	colon:
3	chr6:119253156..119256806-chr6:119394976..119399977,7	K562	blood:
4	chr6:119256349..119258481-chr6:119264695..119266812,2	K562	blood:
5	chr6:119256205..119257932-chr6:119293855..119296677,2	K562	blood:
6	chr6:119213036..119217484-chr6:119254311..119257675,9	MCF-7	breast:
7	chr6:119242613..119249110-chr6:119251513..119257145,6	MCF-7	breast:
8	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
9	chr6:119255727..119258203-chr6:119400226..119402388,2	K562	blood:
10	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
11	chr6:119253238..119258280-chr6:119398045..119402661,8	K562	blood:
12	chr6:119256460..119259122-chr6:119259921..119263121,4	K562	blood:
13	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:
14	chr1:149223435..149224292-chr6:119255876..119256729,2	HCT-116	colon:

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000138772	Chromatin interaction
ENSG00000111879	Chromatin interaction
ENSG00000111875	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1022706	0.97[ASN][1000 genomes]
rs1022707	0.97[ASN][1000 genomes]
rs1022708	0.97[ASN][1000 genomes]
rs1022709	0.97[ASN][1000 genomes]
rs10499090	0.81[ASN][1000 genomes]
rs11153782	0.98[ASN][1000 genomes]
rs11965951	0.98[ASN][1000 genomes]
rs11967231	0.98[ASN][1000 genomes]
rs11967232	0.98[ASN][1000 genomes]
rs12527291	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12527363	0.81[ASN][1000 genomes]
rs1807979	0.98[ASN][1000 genomes]
rs1885125	0.98[ASN][1000 genomes]
rs2145569	0.98[ASN][1000 genomes]
rs2145570	0.98[ASN][1000 genomes]
rs2180860	0.98[ASN][1000 genomes]
rs35906538	0.97[ASN][1000 genomes]
rs3756940	0.81[ASN][1000 genomes]
rs3945959	0.98[ASN][1000 genomes]
rs4245502	0.98[ASN][1000 genomes]
rs4946367	0.82[ASN][1000 genomes]
rs4946369	0.98[ASN][1000 genomes]
rs4946370	0.98[ASN][1000 genomes]
rs4946372	0.98[ASN][1000 genomes]
rs4946373	0.98[ASN][1000 genomes]
rs4946374	0.98[ASN][1000 genomes]
rs4946376	0.98[ASN][1000 genomes]
rs4946377	0.98[ASN][1000 genomes]
rs4946378	0.98[ASN][1000 genomes]
rs4946380	0.94[ASN][1000 genomes]
rs4946381	0.86[ASN][1000 genomes]
rs4946382	0.89[ASN][1000 genomes]
rs4946385	0.85[ASN][1000 genomes]
rs4946386	0.81[ASN][1000 genomes]
rs55978448	0.97[ASN][1000 genomes]
rs56022752	0.92[ASN][1000 genomes]
rs62422265	0.98[ASN][1000 genomes]
rs62422266	0.97[ASN][1000 genomes]
rs62422267	0.98[ASN][1000 genomes]
rs62422268	0.96[ASN][1000 genomes]
rs62422269	0.95[ASN][1000 genomes]
rs62422270	0.97[ASN][1000 genomes]
rs6569035	0.97[ASN][1000 genomes]
rs6901738	0.97[ASN][1000 genomes]
rs6903220	0.97[ASN][1000 genomes]
rs6903579	0.98[ASN][1000 genomes]
rs6904381	0.98[ASN][1000 genomes]
rs6910377	0.98[ASN][1000 genomes]
rs6916168	0.81[ASN][1000 genomes]
rs6916291	0.88[ASN][1000 genomes]
rs6916491	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6916672	0.97[ASN][1000 genomes]
rs6918569	0.97[ASN][1000 genomes]
rs6918844	0.97[ASN][1000 genomes]
rs6919100	0.97[ASN][1000 genomes]
rs6923637	0.97[ASN][1000 genomes]
rs6923771	0.98[ASN][1000 genomes]
rs6928315	0.98[ASN][1000 genomes]
rs6928945	0.98[ASN][1000 genomes]
rs6931423	0.82[ASN][1000 genomes]
rs6933970	0.98[ASN][1000 genomes]
rs6935960	0.98[ASN][1000 genomes]
rs6939937	0.98[ASN][1000 genomes]
rs6940120	0.97[ASN][1000 genomes]
rs72970476	0.81[ASN][1000 genomes]
rs7381533	0.97[ASN][1000 genomes]
rs7381535	0.98[ASN][1000 genomes]
rs7381546	0.98[ASN][1000 genomes]
rs7741149	0.98[ASN][1000 genomes]
rs7758729	0.97[ASN][1000 genomes]
rs7758849	0.96[ASN][1000 genomes]
rs7758862	0.96[ASN][1000 genomes]
rs7759423	0.98[ASN][1000 genomes]
rs9320669	0.98[ASN][1000 genomes]
rs9320670	0.98[ASN][1000 genomes]
rs9320671	0.98[ASN][1000 genomes]
rs9374759	0.97[ASN][1000 genomes]
rs9374763	0.91[ASN][1000 genomes]
rs9374764	0.91[ASN][1000 genomes]
rs9374765	0.88[ASN][1000 genomes]
rs9374766	0.95[ASN][1000 genomes]
rs9374767	0.95[ASN][1000 genomes]
rs9385060	0.94[ASN][1000 genomes]
rs9385063	0.95[ASN][1000 genomes]
rs9387610	0.98[ASN][1000 genomes]
rs9387611	0.96[ASN][1000 genomes]
rs9387612	0.98[ASN][1000 genomes]
rs9387613	0.97[ASN][1000 genomes]
rs9387621	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9401099	0.94[ASN][1000 genomes]
rs9401103	0.96[ASN][1000 genomes]
rs9401106	0.95[ASN][1000 genomes]
rs9489563	0.97[ASN][1000 genomes]
rs9489569	0.97[ASN][1000 genomes]
rs9689589	0.98[ASN][1000 genomes]
rs988098	0.96[ASN][1000 genomes]
rs9968863	0.95[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	esv16596	chr6:119251007-119272087	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv437523	chr6:119251971-119260280	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946371	ASF1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119254000-119257400	Active TSS	GM12878-XiMat	blood
2	chr6:119254600-119257000	Active TSS	Fetal Intestine Large	intestine
3	chr6:119255000-119257000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:119255000-119257000	Active TSS	HMEC	breast
5	chr6:119255000-119257200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:119255000-119257200	Active TSS	Stomach Smooth Muscle	stomach
7	chr6:119255200-119256800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:119255200-119256800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:119255200-119256800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:119255200-119256800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:119255200-119256800	Active TSS	Aorta	Aorta
12	chr6:119255200-119256800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:119255200-119256800	Active TSS	Fetal Muscle Trunk	muscle
14	chr6:119255200-119256800	Active TSS	Fetal Stomach	stomach
15	chr6:119255200-119256800	Active TSS	Right Atrium	heart
16	chr6:119255200-119256800	Active TSS	Right Ventricle	heart
17	chr6:119255200-119256800	Active TSS	Stomach Mucosa	stomach
18	chr6:119255200-119256800	Active TSS	A549	lung
19	chr6:119255200-119257000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:119255200-119257000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:119255200-119257000	Active TSS	HSMMtube	muscle
22	chr6:119255200-119257200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:119255200-119257400	Active TSS	HSMM	muscle
24	chr6:119255400-119256800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:119255400-119256800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:119255400-119256800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:119255400-119256800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr6:119255400-119256800	Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:119255400-119256800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:119255400-119256800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:119255400-119256800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:119255400-119256800	Active TSS	Brain Anterior Caudate	brain
33	chr6:119255400-119256800	Active TSS	Brain Germinal Matrix	brain
34	chr6:119255400-119256800	Active TSS	Brain Hippocampus Middle	brain
35	chr6:119255400-119256800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:119255400-119256800	Active TSS	Brain Substantia Nigra	brain
37	chr6:119255400-119256800	Active TSS	Colonic Mucosa	Colon
38	chr6:119255400-119256800	Active TSS	Ovary	ovary
39	chr6:119255400-119256800	Active TSS	Thymus	Thymus
40	chr6:119255400-119257000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:119255400-119257000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:119255400-119257000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:119255400-119257000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:119255400-119257000	Active TSS	Fetal Intestine Small	intestine
45	chr6:119255400-119257000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:119255400-119257000	Active TSS	Fetal Muscle Leg	muscle
47	chr6:119255400-119257000	Active TSS	K562	blood
48	chr6:119255400-119257000	Active TSS	NHDF-Ad	bronchial
49	chr6:119255400-119257200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:119255400-119257400	Active TSS	Hela-S3	cervix

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