Variant report

Variant	rs6855041
Chromosome Location	chr4:57276451-57276452
allele	A/T
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	MAX	chr4:57276285-57276890	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr4:57276349-57276820	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:57276448-57276874	U87	brain:	n/a	n/a
4	POLR2A	chr4:57276368-57276901	H1-neurons	neurons:	n/a	n/a
5	STAT3	chr4:57276104-57276886	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
6	ATF2	chr4:57276366-57276850	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr4:57276393-57276772	MCF10A-Er-Src	breast:	n/a	n/a
8	GABPA	chr4:57276152-57277216	MCF-7	breast:	n/a	n/a
9	GATA3	chr4:57276313-57276742	T-47D	breast:	n/a	n/a
10	PBX3	chr4:57276246-57276929	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr4:57276299-57277134	H1-neurons	neurons:	n/a	n/a
12	FOSL1	chr4:57276367-57276974	HCT-116	colon:	n/a	n/a
13	ARID3A	chr4:57276375-57276720	HepG2	liver:	n/a	n/a
14	FOXA1	chr4:57276444-57276826	HepG2	liver:	n/a	n/a
15	JUND	chr4:57276400-57276834	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr4:57276332-57276943	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr4:57276197-57276910	MCF-7	breast:	n/a	n/a
18	JUN	chr4:57276446-57276806	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT3	chr4:57276435-57276828	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
20	REST	chr4:57276308-57276980	H1-neurons	neurons:	n/a	n/a
21	GATA3	chr4:57276328-57276692	T-47D	breast:	n/a	n/a
22	FOXA1	chr4:57276428-57276725	T-47D	breast:	n/a	n/a
23	POLR2A	chr4:57276369-57276940	IMR90	lung:	n/a	n/a
24	HDAC2	chr4:57276300-57276823	MCF-7	breast:	n/a	chr4:57276401-57276415
25	YY1	chr4:57276391-57276832	SK-N-SH_RA	brain:	n/a	chr4:57276609-57276628
26	JUN	chr4:57276317-57276845	HUVEC	blood vessel:	n/a	n/a
27	STAT3	chr4:57276417-57276827	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
28	SIN3A	chr4:57276420-57276790	H1-hESC	embryonic stem cell:	n/a	n/a
29	STAT3	chr4:57276435-57276878	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
30	PBX3	chr4:57276352-57276878	SK-N-SH	brain:	n/a	n/a
31	FOS	chr4:57276195-57276903	HUVEC	blood vessel:	n/a	n/a
32	FOSL2	chr4:57276422-57276873	SK-N-SH	brain:	n/a	n/a
33	MAX	chr4:57276441-57276739	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr4:57276403-57276843	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr4:57276431-57276824	PFSK-1	brain:	n/a	n/a
36	SP1	chr4:57276336-57276906	H1-hESC	embryonic stem cell:	n/a	n/a
37	NFIC	chr4:57276001-57276961	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:57276424-57276804	HCT-116	colon:	n/a	n/a
39	MXI1	chr4:57274987-57277307	SK-N-SH	brain:	n/a	chr4:57276622-57276637 chr4:57276620-57276635
40	EP300	chr4:57276425-57276754	SK-N-SH_RA	brain:	n/a	n/a
41	EP300	chr4:57276331-57276726	T-47D	breast:	n/a	n/a
42	GATA1	chr4:57276263-57276734	PBDE	blood:	n/a	n/a
43	YY1	chr4:57276412-57276871	SK-N-SH_RA	brain:	n/a	chr4:57276609-57276628
44	JUND	chr4:57276399-57276824	MCF-7	breast:	n/a	n/a
45	JUND	chr4:57276286-57276885	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr4:57276415-57277013	U87	brain:	n/a	n/a
47	FOSL2	chr4:57276439-57276907	MCF-7	breast:	n/a	n/a
48	SP1	chr4:57276365-57276855	H1-hESC	embryonic stem cell:	n/a	n/a
49	KAP1	chr4:57276382-57276937	U2OS	brain:	n/a	n/a
50	KAP1	chr4:57276378-57276933	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
2	chr4:57274956..57277925-chr4:57332751..57335099,2	MCF-7	breast:
3	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:

Variant related genes	Relation type
ENSG00000268171	TF binding region
PPAT	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10434444	0.81[YRI][hapmap]
rs10434445	0.83[EUR][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12501334	0.86[EUR][1000 genomes]
rs12501502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503412	0.86[EUR][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12510712	0.83[EUR][1000 genomes]
rs1401907	0.91[JPT][hapmap]
rs1474179	0.84[EUR][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967559	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1983378	0.81[YRI][hapmap]
rs2271923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28866881	0.86[EUR][1000 genomes]
rs3796541	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822001	0.81[CEU][hapmap]
rs4493603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864583	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs5010012	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs56392224	0.88[EUR][1000 genomes]
rs58151706	0.86[EUR][1000 genomes]
rs66810706	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820314	0.86[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap]
rs6829250	0.88[EUR][1000 genomes]
rs6832797	0.86[EUR][1000 genomes]
rs6834696	0.90[EUR][1000 genomes]
rs6846895	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7671868	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6855041	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
3	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
7	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
11	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
15	chr4:57270200-57276800	Weak transcription	Colonic Mucosa	Colon
16	chr4:57272200-57276600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:57272400-57276600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:57272600-57276600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:57272800-57276600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:57272800-57276600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:57272800-57276600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
27	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
28	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:57273000-57276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:57273200-57276800	Weak transcription	Hela-S3	cervix
31	chr4:57273400-57276600	Weak transcription	K562	blood
32	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
34	chr4:57274200-57276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:57274200-57296400	Weak transcription	Dnd41	blood
37	chr4:57275000-57276600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:57275000-57278200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr4:57275000-57278400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr4:57275200-57276600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr4:57275200-57276600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr4:57275200-57278000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr4:57275400-57276600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:57275400-57276600	Enhancers	Rectal Smooth Muscle	rectum
45	chr4:57275400-57276600	Enhancers	A549	lung
46	chr4:57275400-57277800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:57275400-57278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:57275400-57278200	Enhancers	NHDF-Ad	bronchial
49	chr4:57275600-57276600	Enhancers	NHEK	skin
50	chr4:57275600-57277000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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