Variant report

Variant	rs341924
Chromosome Location	chr5:77944618-77944619
allele	A/C
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	chr5:77943700-77944754	GM12878	blood:	n/a	chr5:77944086-77944100 chr5:77944085-77944100 chr5:77943943-77943957
2	POLR2A	chr5:77944226-77944884	U87	brain:	n/a	n/a
3	MAX	chr5:77943155-77944694	H1-hESC	embryonic stem cell:	n/a	chr5:77943471-77943481
4	TBP	chr5:77944357-77944659	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:77943265-77945243	GM12892	blood:	n/a	n/a
6	POLR2A	chr5:77943215-77945103	GM18951	blood:	n/a	n/a
7	YY1	chr5:77943800-77945090	GM12878	blood:	n/a	chr5:77944900-77944911 chr5:77944242-77944256 chr5:77944902-77944911 chr5:77944896-77944910 chr5:77944184-77944195 chr5:77944066-77944080 chr5:77944241-77944255 chr5:77944902-77944916 chr5:77944289-77944303 chr5:77944279-77944290 chr5:77944262-77944276 chr5:77944211-77944225
8	POLR2A	chr5:77944328-77944743	U87	brain:	n/a	n/a
9	POLR2A	chr5:77944459-77944734	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr5:77944221-77944757	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr5:77943790-77945102	GM18526	blood:	n/a	n/a
12	MAX	chr5:77943370-77944702	K562	blood:	n/a	chr5:77943471-77943481
13	MXI1	chr5:77943315-77945019	HepG2	liver:	n/a	chr5:77944256-77944265
14	REST	chr5:77943713-77945271	H1-neurons	neurons:	n/a	chr5:77944130-77944144 chr5:77943918-77943931 chr5:77944134-77944147 chr5:77944032-77944039 chr5:77943915-77943928 chr5:77943875-77943888
15	E2F4	chr5:77944026-77944692	MCF10A-Er-Src	breast:	n/a	chr5:77944163-77944178
16	POLR2A	chr5:77942955-77945176	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr5:77943696-77945207	GM19193	blood:	n/a	n/a
18	POLR2A	chr5:77944241-77944742	A549	lung:	n/a	n/a
19	POLR2A	chr5:77943773-77944735	A549	lung:	n/a	n/a
20	POLR2A	chr5:77944232-77944680	U87	brain:	n/a	n/a
21	POLR2A	chr5:77943092-77946191	HepG2	liver:	n/a	n/a
22	HMGN3	chr5:77943764-77945119	K562	blood:	n/a	n/a
23	CHD2	chr5:77944340-77945022	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:77944380-77944673	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:77944423-77944701	HepG2	liver:	n/a	n/a
26	TAF1	chr5:77944251-77944777	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr5:77942997-77945191	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:77943680-77945129	MCF-7	breast:	n/a	n/a
29	YY1	chr5:77943888-77944729	GM12878	blood:	n/a	chr5:77944242-77944256 chr5:77944184-77944195 chr5:77944066-77944080 chr5:77944241-77944255 chr5:77944289-77944303 chr5:77944279-77944290 chr5:77944262-77944276 chr5:77944211-77944225
30	RAD21	chr5:77943662-77944854	SK-N-SH_RA	brain:	n/a	chr5:77944799-77944811
31	ZBTB7A	chr5:77944049-77944806	K562	blood:	n/a	chr5:77944251-77944262
32	EGR1	chr5:77944358-77944770	ECC-1	luminal epithelium:	n/a	chr5:77944520-77944534 chr5:77944476-77944490
33	POLR2A	chr5:77943225-77944771	Hela-S3	cervix:	n/a	n/a
34	HEY1	chr5:77944365-77945028	HepG2	liver:	n/a	chr5:77945005-77945020 chr5:77944894-77944909 chr5:77944892-77944907
35	POLR2A	chr5:77943207-77945094	HepG2	liver:	n/a	n/a
36	CTCF	chr5:77944520-77944670	GM12873	blood:	n/a	n/a
37	POLR2A	chr5:77943210-77945277	GM18505	blood:	n/a	n/a
38	TAF1	chr5:77944212-77944976	H1-hESC	embryonic stem cell:	n/a	n/a
39	JUND	chr5:77943599-77944640	A549	lung:	n/a	n/a
40	SIN3AK20	chr5:77943812-77945242	PANC-1	pancreas:	n/a	n/a
41	TAF1	chr5:77944254-77944672	A549	lung:	n/a	n/a
42	CEBPD	chr5:77944264-77944761	HepG2	liver:	n/a	n/a
43	MAZ	chr5:77943814-77944791	HepG2	liver:	n/a	n/a
44	MAX	chr5:77943122-77944759	HepG2	liver:	n/a	chr5:77943471-77943481
45	ZBTB7A	chr5:77944106-77945417	ECC-1	luminal epithelium:	n/a	chr5:77944251-77944262 chr5:77945154-77945161
46	POLR2A	chr5:77943060-77944990	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr5:77944296-77944716	Hela-S3	cervix:	n/a	n/a
48	SMARCB1	chr5:77943211-77945306	Hela-S3	cervix:	n/a	n/a
49	HEY1	chr5:77944460-77944702	HepG2	liver:	n/a	n/a
50	POLR2A	chr5:77944367-77944786	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:77932938..77939935-chr5:77942023..77946135,10	MCF-7	breast:
2	chr5:77936618..77938171-chr5:77943031..77945738,2	K562	blood:

Variant related genes	Relation type
LHFPL2	TF binding region
HMGB1P21	TF binding region
ENSG00000145685	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10060702	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs163633	0.92[ASN][1000 genomes]
rs168190	0.91[ASN][1000 genomes]
rs171035	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs189322	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs341917	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs341918	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs341919	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs341920	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs341925	0.92[ASN][1000 genomes]
rs341926	0.94[ASN][1000 genomes]
rs341927	0.92[ASN][1000 genomes]
rs341928	0.90[ASN][1000 genomes]
rs341930	0.89[ASN][1000 genomes]
rs344639	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461989	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522738	chr5:77434730-78063683	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3522739	chr5:77434730-78063683	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv949530	chr5:77830403-78477017	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv830356	chr5:77847022-78011999	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1021768	chr5:77881915-78465489	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2762527	chr5:77921199-78548196	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv1792242	chr5:77927033-77966625	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1841124	chr5:77937453-77944988	Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv528833	chr5:77937453-78016860	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv598701	chr5:77940790-77944988	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv3439355	chr5:77943421-77945969	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv12753	chr5:77943975-77945033	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv598702	chr5:77944003-77944829	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv598703	chr5:77944003-77944883	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv598704	chr5:77944003-77944988	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1795250	chr5:77944003-77949565	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv1846202	chr5:77944003-77949565	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv598705	chr5:77944054-77944644	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv598706	chr5:77944054-77944718	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv598707	chr5:77944054-77944935	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv598708	chr5:77944157-77944718	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv598709	chr5:77944157-77944935	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv598710	chr5:77944157-77944988	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv598711	chr5:77944208-77944935	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv598712	chr5:77944208-77944988	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:77941600-77945200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:77942200-77945000	Active TSS	GM12878-XiMat	blood
3	chr5:77942200-77945200	Active TSS	HSMMtube	muscle
4	chr5:77942200-77945400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:77942200-77945400	Active TSS	Rectal Smooth Muscle	rectum
6	chr5:77942200-77945600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:77942200-77945800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr5:77942600-77945200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:77942600-77945200	Active TSS	Fetal Stomach	stomach
10	chr5:77942600-77945400	Active TSS	Aorta	Aorta
11	chr5:77942600-77945400	Active TSS	Ovary	ovary
12	chr5:77942800-77945000	Active TSS	HMEC	breast
13	chr5:77942800-77945200	Active TSS	HSMM	muscle
14	chr5:77942800-77945200	Active TSS	NHLF	lung
15	chr5:77942800-77945400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:77942800-77945400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:77942800-77945400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr5:77942800-77945400	Active TSS	NHDF-Ad	bronchial
19	chr5:77942800-77945600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:77942800-77945600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:77942800-77945800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr5:77943000-77945000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr5:77943000-77945000	Active TSS	Fetal Intestine Small	intestine
24	chr5:77943000-77945200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:77943000-77945200	Active TSS	A549	lung
26	chr5:77943000-77945400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:77943000-77945400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:77943000-77945400	Active TSS	Fetal Intestine Large	intestine
29	chr5:77943000-77945400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr5:77943000-77945600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr5:77943000-77945800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr5:77943000-77945800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr5:77943000-77946000	Active TSS	Fetal Kidney	kidney
34	chr5:77943200-77945200	Active TSS	Lung	lung
35	chr5:77943200-77945400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:77943200-77945400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:77943200-77945400	Active TSS	Colon Smooth Muscle	Colon
38	chr5:77943200-77945600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:77943200-77945600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:77943200-77945600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:77943200-77945600	Active TSS	HepG2	liver
42	chr5:77943200-77945800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr5:77943400-77945000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr5:77943400-77945000	Active TSS	Fetal Muscle Leg	muscle
45	chr5:77943400-77945000	Active TSS	NHEK	skin
46	chr5:77943400-77945200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:77943400-77945200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:77943400-77945200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr5:77943400-77945200	Active TSS	Gastric	stomach
50	chr5:77943400-77945200	Active TSS	Placenta Amnion	Placenta Amnion

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