Variant report

Variant	rs6896940
Chromosome Location	chr5:178985994-178985995
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	CHD1	chr5:178985618-178986945	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr5:178985457-178987460	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:178985798-178987122	GM12878	blood:	n/a	n/a
4	TAF1	chr5:178985924-178986941	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr5:178985889-178987010	A549	lung:	n/a	n/a
6	MAX	chr5:178985914-178987175	SK-N-SH	brain:	n/a	n/a
7	FOS	chr5:178985946-178986742	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr5:178985994-178986942	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:178985969-178987012	SK-N-MC	brain:	n/a	n/a
10	MYC	chr5:178985923-178987048	MCF10A-Er-Src	breast:	n/a	n/a
11	REST	chr5:178985943-178986182	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:178985826-178987315	SK-N-MC	brain:	n/a	n/a
13	ATF2	chr5:178985934-178986763	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:178985741-178987115	PANC-1	pancreas:	n/a	n/a
15	YY1	chr5:178985933-178986892	SK-N-SH	brain:	n/a	chr5:178986551-178986559
16	FOXA2	chr5:178985821-178986222	A549	lung:	n/a	n/a
17	YY1	chr5:178985949-178986946	SK-N-SH_RA	brain:	n/a	chr5:178986551-178986559
18	JUND	chr5:178985893-178986979	H1-hESC	embryonic stem cell:	n/a	n/a
19	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
20	E2F4	chr5:178985857-178986863	MCF10A-Er-Src	breast:	n/a	n/a
21	CHD2	chr5:178985950-178986993	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:178985838-178987112	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr5:178985895-178986810	GM12878	blood:	n/a	n/a
24	STAT5A	chr5:178985919-178986361	GM12878	blood:	n/a	n/a
25	PML	chr5:178985993-178987118	MCF-7	breast:	n/a	chr5:178986488-178986496
26	POLR2A	chr5:178985734-178987380	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr5:178985949-178987287	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr5:178985900-178987269	ECC-1	luminal epithelium:	n/a	n/a
29	MAX	chr5:178985887-178987449	MCF-7	breast:	n/a	n/a
30	PML	chr5:178985935-178986872	GM12878	blood:	n/a	chr5:178986488-178986496
31	POLR2A	chr5:178985809-178986865	HUVEC	blood vessel:	n/a	n/a
32	FOXA1	chr5:178985769-178986315	HepG2	liver:	n/a	n/a
33	KAP1	chr5:178985949-178986587	U2OS	brain:	n/a	chr5:178986488-178986496
34	MAX	chr5:178985938-178987205	MCF-7	breast:	n/a	n/a
35	TBL1XR1	chr5:178985914-178986088	K562	blood:	n/a	n/a
36	KAP1	chr5:178985799-178986362	K562	blood:	n/a	n/a
37	POLR2A	chr5:178985916-178986864	GM12892	blood:	n/a	n/a
38	E2F6	chr5:178985989-178986340	A549	lung:	n/a	n/a
39	POLR2A	chr5:178985492-178987032	GM12878	blood:	n/a	n/a
40	SP1	chr5:178985794-178987035	H1-hESC	embryonic stem cell:	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
41	NRF1	chr5:178985981-178986696	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr5:178985609-178987283	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr5:178985891-178987186	U87	brain:	n/a	n/a
44	TCF12	chr5:178985948-178986360	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr5:178985840-178987133	GM18505	blood:	n/a	n/a
46	MYC	chr5:178985964-178986855	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr5:178985964-178987029	GM18951	blood:	n/a	n/a
48	POLR2A	chr5:178985862-178986923	HL-60	blood:	n/a	n/a
49	POLR2A	chr5:178985862-178987120	GM12878	blood:	n/a	n/a
50	SRF	chr5:178985927-178987463	MCF-7	breast:	n/a	n/a

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

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

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10064596	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10074573	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10078712	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[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];0.98[ASN][1000 genomes]
rs12652495	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12658664	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13179470	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183521	0.86[ASN][1000 genomes]
rs4700835	0.88[ASN][1000 genomes]
rs4700836	0.88[ASN][1000 genomes]
rs4701130	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4701131	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4701132	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601050	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6895321	0.81[ASN][1000 genomes]
rs6896112	0.88[ASN][1000 genomes]
rs7702303	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703730	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7718673	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7723230	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7733389	0.84[ASN][1000 genomes]
rs7736163	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[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
rs6896940	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178978600-178986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:178978800-178986000	Weak transcription	Aorta	Aorta
3	chr5:178978800-178986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:178979600-178986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:178979800-178986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:178980400-178986000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:178980400-178986000	Weak transcription	Colonic Mucosa	Colon
8	chr5:178980400-178986000	Weak transcription	Placenta	Placenta
9	chr5:178980400-178986200	Weak transcription	Gastric	stomach
10	chr5:178980600-178986000	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:178981000-178986000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:178981000-178986000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:178981200-178986000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:178981200-178986000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:178981200-178986000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:178981200-178986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:178981200-178986000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:178981200-178986000	Weak transcription	Brain Angular Gyrus	brain
19	chr5:178981200-178986000	Weak transcription	Left Ventricle	heart
20	chr5:178981200-178986000	Weak transcription	Ovary	ovary
21	chr5:178981200-178986000	Weak transcription	Psoas Muscle	Psoas
22	chr5:178981200-178986200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:178981200-178986200	Weak transcription	Lung	lung
24	chr5:178981200-178996200	Weak transcription	K562	blood
25	chr5:178981400-178986000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:178981400-178986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:178981400-178986000	Weak transcription	Hela-S3	cervix
28	chr5:178981600-178986000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:178981600-178986000	Weak transcription	Right Ventricle	heart
30	chr5:178981600-178986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:178981600-178986200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:178982400-178986200	Weak transcription	Spleen	Spleen
33	chr5:178982400-178986400	Weak transcription	Small Intestine	intestine
34	chr5:178982400-178986400	Weak transcription	Dnd41	blood
35	chr5:178982600-178986000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:178985000-178986000	Enhancers	Liver	Liver
37	chr5:178985400-178986000	Enhancers	Fetal Muscle Trunk	muscle
38	chr5:178985400-178986000	Enhancers	Thymus	Thymus
39	chr5:178985600-178986000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr5:178985600-178986000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr5:178985600-178986000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr5:178985600-178986000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:178985600-178986000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr5:178985600-178986000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr5:178985600-178986000	Enhancers	Primary B cells from cord blood	blood
46	chr5:178985600-178986000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr5:178985600-178986000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:178985600-178986000	Flanking Active TSS	Fetal Brain Female	brain
49	chr5:178985600-178986000	Weak transcription	Pancreas	Pancrea
50	chr5:178985600-178986000	Enhancers	Placenta Amnion	Placenta Amnion

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