Variant report

Variant	rs16846478
Chromosome Location	chr1:173832647-173832648
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	POLR2A	chr1:173830742-173838152	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:173830604-173834319	HL-60	blood:	n/a	n/a
3	SIN3AK20	chr1:173832523-173832719	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:173829652-173834370	K562	blood:	n/a	n/a
5	TAF1	chr1:173832314-173832767	PFSK-1	brain:	n/a	n/a
6	RCOR1	chr1:173831939-173832682	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
8	PBX3	chr1:173830728-173832741	SK-N-SH	brain:	n/a	n/a
9	CEBPD	chr1:173830788-173832895	K562	blood:	n/a	n/a
10	BCLAF1	chr1:173831688-173832909	K562	blood:	n/a	chr1:173831994-173832003
11	POLR2A	chr1:173829381-173833686	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
13	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
14	ATF3	chr1:173832277-173833019	A549	lung:	n/a	n/a
15	CCNT2	chr1:173831768-173832913	K562	blood:	n/a	chr1:173832018-173832027
16	POLR2A	chr1:173830571-173832892	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:173830687-173832742	Raji	blood:	n/a	n/a
18	USF1	chr1:173832296-173832824	A549	lung:	n/a	n/a
19	STAT5A	chr1:173831559-173832855	GM12878	blood:	n/a	chr1:173832020-173832032 chr1:173831994-173832005 chr1:173832018-173832030
20	POLR2A	chr1:173829861-173834161	K562	blood:	n/a	n/a
21	POLR2A	chr1:173829985-173833751	GM19193	blood:	n/a	n/a
22	ELK1	chr1:173832080-173832992	K562	blood:	n/a	n/a
23	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
24	POLR2A	chr1:173828233-173834504	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:173830753-173833030	HCT-116	colon:	n/a	n/a
26	JUND	chr1:173830702-173832980	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:173829284-173838362	K562	blood:	n/a	n/a
28	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
29	CHD1	chr1:173831798-173837941	IMR90	lung:	n/a	chr1:173836993-173837000 chr1:173837608-173837618 chr1:173837832-173837842
30	BCLAF1	chr1:173831672-173832655	GM12878	blood:	n/a	chr1:173831994-173832003
31	POLR2A	chr1:173829663-173838350	K562	blood:	n/a	n/a
32	POLR2A	chr1:173829737-173838261	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr1:173829767-173838193	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:173829946-173832856	NB4	blood:	n/a	n/a
35	JUN	chr1:173832403-173840952	K562	blood:	n/a	chr1:173837048-173837062 chr1:173840939-173840951 chr1:173837421-173837430 chr1:173837165-173837178 chr1:173837443-173837452 chr1:173833568-173833581 chr1:173837835-173837844 chr1:173840672-173840683 chr1:173837169-173837178
36	MTA3	chr1:173830550-173833227	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:173829033-173834330	U87	brain:	n/a	n/a
38	POLR2A	chr1:173829700-173838480	GM18505	blood:	n/a	n/a
39	MAFF	chr1:173831943-173832783	K562	blood:	n/a	n/a
40	ZMIZ1	chr1:173832360-173832942	K562	blood:	n/a	n/a
41	POLR2A	chr1:173830001-173838163	GM12892	blood:	n/a	n/a
42	POLR2A	chr1:173830619-173832854	HL-60	blood:	n/a	n/a
43	CHD2	chr1:173831699-173832931	Hela-S3	cervix:	n/a	n/a
44	CHD2	chr1:173830791-173832679	K562	blood:	n/a	n/a
45	TEAD4	chr1:173831595-173832881	K562	blood:	n/a	n/a
46	NRF1	chr1:173831777-173832980	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:173829851-173834486	H1-hESC	embryonic stem cell:	n/a	n/a
48	PML	chr1:173829815-173833119	K562	blood:	n/a	n/a
49	PBX3	chr1:173830648-173832811	A549	lung:	n/a	n/a
50	TEAD4	chr1:173831746-173832848	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173831929..173834882-chr1:173882309..173883868,2	MCF-7	breast:
2	chr1:173829871..173833250-chr1:173884943..173888028,3	K562	blood:
3	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
4	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:
5	chr1:173832421..173839801-chr1:173885332..173891780,9	MCF-7	breast:
6	chr1:173831906..173839548-chr1:173987374..173993282,15	MCF-7	breast:
7	chr1:173793576..173795606-chr1:173831172..173833639,2	MCF-7	breast:
8	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
9	chr1:173445658..173447676-chr1:173831376..173834939,3	K562	blood:
10	chr1:173682967..173685869-chr1:173831317..173832954,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DARS2-1	chr1:173832364-173833079	XLOC_000467
2	lnc-SERPINC1-1	chr1:173827684-173834420	NONHSAT007659
3	lnc-DARS2-1	chr1:173832386-173833079	ENSG00000270084.1

Variant related genes	Relation type
ZBTB37	TF binding region
ENSG00000117593	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000252231	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000236535	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16846418	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846433	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846526	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846546	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846561	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2065170	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2068871	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2146372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227589	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2227592	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759328	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791022	0.88[ASN][1000 genomes]
rs57022387	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58994962	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61262741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61649485	0.88[ASN][1000 genomes]
rs6656255	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696381	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941987	0.83[EUR][1000 genomes]
rs941988	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9970048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
3	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
6	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
12	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:173821000-173834000	Strong transcription	Liver	Liver
16	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:173822000-173834000	Strong transcription	Fetal Intestine Large	intestine
18	chr1:173822400-173833600	Strong transcription	Fetal Brain Female	brain
19	chr1:173822400-173833800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:173822800-173833400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:173823200-173833400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:173824600-173833800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:173824800-173834600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:173827000-173833800	Weak transcription	HepG2	liver
27	chr1:173827400-173834400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:173827600-173833400	Strong transcription	Fetal Intestine Small	intestine
29	chr1:173827600-173834000	Weak transcription	Psoas Muscle	Psoas
30	chr1:173827800-173834400	Strong transcription	Fetal Stomach	stomach
31	chr1:173828600-173833200	Strong transcription	Dnd41	blood
32	chr1:173829400-173833200	Strong transcription	Primary T cells from cord blood	blood
33	chr1:173829400-173834600	Strong transcription	Brain Anterior Caudate	brain
34	chr1:173829600-173833000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:173829600-173834600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:173829600-173835600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:173830000-173833000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:173830000-173834000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:173830000-173834000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:173830400-173834000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:173830600-173833800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:173830800-173833400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:173830800-173834800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:173830800-173835000	Strong transcription	Ovary	ovary
45	chr1:173830800-173835800	Strong transcription	Placenta	Placenta
46	chr1:173831000-173833000	Strong transcription	Osteobl	bone
47	chr1:173831000-173833600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:173831000-173834200	Strong transcription	Thymus	Thymus
49	chr1:173831000-173834400	Strong transcription	Brain Hippocampus Middle	brain
50	chr1:173831000-173834600	Strong transcription	Fetal Lung	lung

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