Variant report

Variant	rs6601050
Chromosome Location	chr5:178986261-178986262
allele	C/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	YY1	chr5:178986258-178986912	ECC-1	luminal epithelium:	n/a	chr5:178986551-178986559
2	CHD1	chr5:178985618-178986945	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr5:178985457-178987460	SK-N-SH	brain:	n/a	n/a
4	SIN3AK20	chr5:178986065-178987144	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr5:178985798-178987122	GM12878	blood:	n/a	n/a
6	TAF1	chr5:178985924-178986941	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:178986257-178987131	Gliobla	brain:	n/a	n/a
8	CEBPB	chr5:178985889-178987010	A549	lung:	n/a	n/a
9	POLR2A	chr5:178986261-178987092	A549	lung:	n/a	n/a
10	YY1	chr5:178986258-178986664	GM12892	blood:	n/a	chr5:178986551-178986559
11	SP1	chr5:178986183-178987120	A549	lung:	n/a	chr5:178986611-178986625 chr5:178986510-178986519 chr5:178986509-178986518 chr5:178986510-178986519 chr5:178986616-178986625 chr5:178986615-178986624 chr5:178986614-178986626 chr5:178986614-178986626
12	MAX	chr5:178985914-178987175	SK-N-SH	brain:	n/a	n/a
13	FOS	chr5:178985946-178986742	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr5:178985994-178986942	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:178986194-178987011	GM12892	blood:	n/a	n/a
16	SP4	chr5:178986008-178987045	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:178985969-178987012	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr5:178986166-178987190	H1-neurons	neurons:	n/a	n/a
19	MYC	chr5:178985923-178987048	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr5:178985826-178987315	SK-N-MC	brain:	n/a	n/a
21	ATF2	chr5:178985934-178986763	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:178985741-178987115	PANC-1	pancreas:	n/a	n/a
23	YY1	chr5:178985933-178986892	SK-N-SH	brain:	n/a	chr5:178986551-178986559
24	YY1	chr5:178986228-178986836	A549	lung:	n/a	chr5:178986551-178986559
25	YY1	chr5:178985949-178986946	SK-N-SH_RA	brain:	n/a	chr5:178986551-178986559
26	POLR2A	chr5:178986007-178986911	GM12891	blood:	n/a	n/a
27	JUND	chr5:178985893-178986979	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP1	chr5:178985918-178987320	HCT-116	colon:	n/a	chr5:178986611-178986625 chr5:178986510-178986519 chr5:178986509-178986518 chr5:178986510-178986519 chr5:178986616-178986625 chr5:178986615-178986624 chr5:178986614-178986626 chr5:178986614-178986626
29	POLR2A	chr5:178986199-178987194	HL-60	blood:	n/a	n/a
30	TAF1	chr5:178986259-178986913	PFSK-1	brain:	n/a	n/a
31	E2F4	chr5:178985857-178986863	MCF10A-Er-Src	breast:	n/a	n/a
32	ELF1	chr5:178986181-178986923	MCF-7	breast:	n/a	n/a
33	CHD2	chr5:178985950-178986993	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:178986201-178987054	HepG2	liver:	n/a	n/a
35	POLR2A	chr5:178985838-178987112	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr5:178985895-178986810	GM12878	blood:	n/a	n/a
37	FOSL2	chr5:178986036-178986974	A549	lung:	n/a	n/a
38	STAT5A	chr5:178985919-178986361	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr5:178986210-178987135	A549	lung:	n/a	n/a
40	PML	chr5:178985993-178987118	MCF-7	breast:	n/a	chr5:178986488-178986496
41	POLR2A	chr5:178985734-178987380	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr5:178986026-178987152	HepG2	liver:	n/a	n/a
43	TAF1	chr5:178985949-178987287	H1-hESC	embryonic stem cell:	n/a	n/a
44	GABPA	chr5:178986095-178987067	MCF-7	breast:	n/a	n/a
45	MAX	chr5:178985900-178987269	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr5:178985887-178987449	MCF-7	breast:	n/a	n/a
47	POLR2A	chr5:178986188-178987235	HepG2	liver:	n/a	n/a
48	PML	chr5:178985935-178986872	GM12878	blood:	n/a	chr5:178986488-178986496
49	POLR2A	chr5:178985809-178986865	HUVEC	blood vessel:	n/a	n/a
50	FOXA1	chr5:178985769-178986315	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178986094..178988194-chr5:179049451..179052935,4	MCF-7	breast:
2	chr5:178984878..178986642-chr5:178988155..178989998,2	MCF-7	breast:
3	chr5:177630883..177632521-chr5:178985029..178986804,2	MCF-7	breast:
4	chr5:178985235..178987908-chr5:179124412..179127341,2	MCF-7	breast:
5	chr5:178984205..178987569-chr5:178988108..178992792,6	MCF-7	breast:
6	chr5:178984896..178986468-chr5:179223868..179225684,2	MCF-7	breast:
7	chr5:178984558..178987542-chr5:178988263..178990973,3	K562	blood:
8	chr15:101835145..101835812-chr5:178986003..178986591,2	HCT-116	colon:
9	chr5:178966269..178968602-chr5:178984458..178986550,2	MCF-7	breast:
10	chr5:178984119..178986610-chr5:178999493..179002273,3	K562	blood:
11	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:
12	chr5:178977809..178978321-chr5:178985908..178986661,2	MCF-7	breast:

Variant related genes	Relation type
RUFY1	TF binding region
ENSG00000259172	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000131876	Chromatin interaction
ENSG00000221394	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10064596	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10074573	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10078712	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078796	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10479542	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12652495	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12658664	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13179470	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183521	0.87[ASN][1000 genomes]
rs4131080	0.85[CEU][hapmap]
rs4700835	0.89[ASN][1000 genomes]
rs4700836	0.89[ASN][1000 genomes]
rs4701130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6889447	0.86[CHB][hapmap]
rs6895321	0.82[ASN][1000 genomes]
rs6896112	0.89[ASN][1000 genomes]
rs6896940	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7702303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7718673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7723230	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7733389	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7736163	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][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	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
6	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
7	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
10	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6601050	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178981200-178996200	Weak transcription	K562	blood
2	chr5:178982400-178986400	Weak transcription	Small Intestine	intestine
3	chr5:178982400-178986400	Weak transcription	Dnd41	blood
4	chr5:178985600-178986400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:178985600-178986400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:178985600-178986400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:178985600-178986400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr5:178985600-178986400	Flanking Active TSS	HUVEC	blood vessel
9	chr5:178985600-178986800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:178985600-178986800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr5:178985600-178987000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:178985600-178987000	Active TSS	Brain Germinal Matrix	brain
13	chr5:178985600-178987000	Active TSS	HSMM	muscle
14	chr5:178985600-178987200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:178985600-178987400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:178985600-178987400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:178985600-178987600	Active TSS	A549	lung
18	chr5:178985800-178986400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr5:178985800-178986400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr5:178985800-178986400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:178985800-178986400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:178985800-178986400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr5:178985800-178986400	Flanking Active TSS	Fetal Brain Male	brain
24	chr5:178985800-178986400	Flanking Active TSS	Osteobl	bone
25	chr5:178985800-178986600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:178985800-178986800	Active TSS	Duodenum Mucosa	Duodenum
27	chr5:178985800-178986800	Active TSS	Rectal Smooth Muscle	rectum
28	chr5:178985800-178986800	Active TSS	HSMMtube	muscle
29	chr5:178985800-178986800	Active TSS	NH-A	brain
30	chr5:178985800-178987000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr5:178985800-178987000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr5:178985800-178987000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:178985800-178987000	Active TSS	Brain Cingulate Gyrus	brain
34	chr5:178985800-178987000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:178985800-178987000	Active TSS	Brain Substantia Nigra	brain
36	chr5:178985800-178987000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr5:178985800-178987000	Active TSS	Fetal Lung	lung
38	chr5:178985800-178987000	Active TSS	Fetal Stomach	stomach
39	chr5:178985800-178987000	Active TSS	Right Atrium	heart
40	chr5:178985800-178987000	Active TSS	GM12878-XiMat	blood
41	chr5:178985800-178987000	Active TSS	NHDF-Ad	bronchial
42	chr5:178985800-178987000	Active TSS	NHLF	lung
43	chr5:178985800-178987200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr5:178985800-178987200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:178985800-178987200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr5:178985800-178987200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:178985800-178987200	Active TSS	Fetal Intestine Large	intestine
48	chr5:178985800-178987400	Active TSS	H9 Cell Line	embryonic stem cell
49	chr5:178985800-178987400	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:178985800-178987400	Active TSS	HUES6 Cell Line	embryonic stem cell

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