Variant report

Variant	rs16835714
Chromosome Location	chr1:150254974-150254975
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	RFX5	chr1:150254676-150254982	K562	blood:	n/a	chr1:150254855-150254864
2	STAT5A	chr1:150254227-150255040	GM12878	blood:	n/a	n/a
3	E2F4	chr1:150254673-150255008	MCF10A-Er-Src	breast:	n/a	chr1:150254751-150254760
4	POLR2A	chr1:150254837-150255308	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr1:150254767-150255473	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr1:150254479-150254977	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr1:150253990-150255512	ECC-1	luminal epithelium:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
8	MYC	chr1:150254703-150255024	HUVEC	blood vessel:	n/a	chr1:150254829-150254848 chr1:150254834-150254843 chr1:150254836-150254843
9	USF1	chr1:150254237-150255187	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
10	POLR2A	chr1:150253538-150255531	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr1:150253599-150255218	A549	lung:	n/a	chr1:150254751-150254760
12	USF1	chr1:150254468-150255069	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
13	FOXA1	chr1:150254653-150255055	T-47D	breast:	n/a	n/a
14	USF1	chr1:150254563-150255144	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
15	EP300	chr1:150254518-150255044	T-47D	breast:	n/a	n/a
16	MXI1	chr1:150253414-150255748	IMR90	lung:	n/a	n/a
17	USF1	chr1:150254584-150255350	H1-hESC	embryonic stem cell:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
18	BHLHE40	chr1:150254235-150255339	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254892-150254901
19	CREB1	chr1:150254180-150255378	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:150254827-150255226	U87	brain:	n/a	n/a
21	POLR2A	chr1:150254140-150255558	H1-neurons	neurons:	n/a	n/a
22	TCF12	chr1:150254726-150255020	H1-hESC	embryonic stem cell:	n/a	n/a
23	E2F6	chr1:150254136-150255041	A549	lung:	n/a	chr1:150254751-150254760
24	SP1	chr1:150254287-150255531	H1-hESC	embryonic stem cell:	n/a	chr1:150254925-150254939 chr1:150254928-150254940 chr1:150254947-150254958 chr1:150254929-150254938 chr1:150254930-150254939 chr1:150254853-150254874 chr1:150254928-150254940 chr1:150254788-150254795 chr1:150254919-150254933 chr1:150254930-150254939 chr1:150254929-150254939 chr1:150254929-150254939 chr1:150254928-150254939 chr1:150255181-150255195
25	MAX	chr1:150253731-150255474	H1-hESC	embryonic stem cell:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
26	POLR2A	chr1:150253635-150255360	U87	brain:	n/a	n/a
27	JUND	chr1:150253740-150255021	H1-hESC	embryonic stem cell:	n/a	n/a
28	USF1	chr1:150254700-150255106	K562	blood:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
29	MYC	chr1:150253592-150255167	MCF10A-Er-Src	breast:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
30	FOXA2	chr1:150254514-150255197	A549	lung:	n/a	n/a
31	MAZ	chr1:150253610-150255847	IMR90	lung:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
32	USF1	chr1:150254199-150255342	H1-hESC	embryonic stem cell:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
33	USF1	chr1:150254144-150255443	ECC-1	luminal epithelium:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
34	MAX	chr1:150254137-150255194	SK-N-SH	brain:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
35	POLR2A	chr1:150253579-150255360	U87	brain:	n/a	n/a
36	POLR2A	chr1:150254765-150255262	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr1:150254103-150255411	MCF-7	breast:	n/a	n/a
38	USF2	chr1:150254240-150255277	H1-hESC	embryonic stem cell:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254892-150254901
39	USF1	chr1:150254120-150255131	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
40	USF1	chr1:150254161-150255203	A549	lung:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
41	SIN3AK20	chr1:150254907-150255301	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr1:150254161-150255090	GM12878	blood:	n/a	chr1:150254466-150254475 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150254468-150254484 chr1:150254836-150254843
43	CHD2	chr1:150253820-150255404	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOXA1	chr1:150254604-150255010	T-47D	breast:	n/a	n/a
45	RFX5	chr1:150254323-150254990	H1-hESC	embryonic stem cell:	n/a	chr1:150254855-150254864
46	TBP	chr1:150253705-150255232	H1-hESC	embryonic stem cell:	n/a	n/a
47	USF1	chr1:150254657-150255001	GM12878	blood:	n/a	chr1:150254892-150254901 chr1:150254891-150254900 chr1:150254832-150254843 chr1:150254892-150254901
48	MAX	chr1:150253764-150255180	A549	lung:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
49	TAF1	chr1:150254234-150255560	H1-neurons	neurons:	n/a	n/a
50	CREB1	chr1:150254146-150255374	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150226594..150229990-chr1:150253466..150255722,4	K562	blood:
2	chr1:150252708..150255493-chr1:150334761..150336728,2	K562	blood:
3	chr1:144532574..144534383-chr1:150253333..150256090,2	K562	blood:
4	chr1:150254809..150257635-chr11:62608044..62609557,2	MCF-7	breast:
5	chr1:150254416..150258326-chr1:150293142..150296194,3	K562	blood:
6	chr1:150252847..150256677-chr1:150333609..150339009,8	MCF-7	breast:
7	chr1:149856618..149859874-chr1:150252392..150257192,4	MCF-7	breast:
8	chr1:149982260..149984112-chr1:150253669..150255654,2	MCF-7	breast:
9	chr1:150252171..150257673-chr1:150291650..150295636,15	MCF-7	breast:
10	chr1:150254103..150255766-chr1:150487973..150490880,2	MCF-7	breast:
11	chr1:150226746..150229990-chr1:150252728..150255652,4	K562	blood:
12	chr1:150254313..150256354-chr20:49126871..49128385,2	MCF-7	breast:
13	chr1:150253619..150256471-chr1:150290811..150295516,7	MCF-7	breast:
14	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:
15	chr1:150232148..150235043-chr1:150254020..150257209,3	K562	blood:

Variant related genes	Relation type
C1orf51	TF binding region
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000196396	Chromatin interaction
ENSG00000228126	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000238526	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16835698	1.00[YRI][hapmap]
rs16835872	1.00[YRI][hapmap]
rs16835995	1.00[YRI][hapmap]
rs16836615	1.00[YRI][hapmap]
rs16836849	1.00[YRI][hapmap]
rs16836939	1.00[YRI][hapmap]
rs16837013	1.00[YRI][hapmap]
rs16837048	1.00[YRI][hapmap]
rs56871849	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150252600-150255600	Flanking Active TSS	Liver	Liver
2	chr1:150253400-150255200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:150253400-150255400	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr1:150253400-150255600	Active TSS	Colon Smooth Muscle	Colon
5	chr1:150253400-150256000	Active TSS	Right Atrium	heart
6	chr1:150253400-150256000	Flanking Active TSS	HMEC	breast
7	chr1:150253600-150255000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:150253600-150255000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:150253600-150255000	Active TSS	A549	lung
10	chr1:150253600-150255200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:150253600-150255200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:150253600-150255200	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:150253600-150255200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:150253600-150255400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:150253600-150255400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:150253600-150255600	Active TSS	Brain Anterior Caudate	brain
17	chr1:150253600-150255600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:150253600-150255600	Active TSS	NHDF-Ad	bronchial
19	chr1:150253600-150255800	Active TSS	Brain Angular Gyrus	brain
20	chr1:150253600-150256200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:150253600-150256200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:150253800-150255000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:150253800-150255000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
24	chr1:150253800-150255000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:150253800-150255000	Active TSS	Brain Germinal Matrix	brain
26	chr1:150253800-150255000	Active TSS	Brain Hippocampus Middle	brain
27	chr1:150253800-150255000	Active TSS	Esophagus	oesophagus
28	chr1:150253800-150255200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:150253800-150255200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr1:150253800-150255200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:150253800-150255200	Active TSS	Left Ventricle	heart
32	chr1:150253800-150255400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr1:150253800-150255400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:150253800-150255400	Active TSS	Fetal Heart	heart
35	chr1:150253800-150255400	Active TSS	Gastric	stomach
36	chr1:150253800-150255600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:150253800-150255600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:150253800-150255600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:150253800-150255600	Active TSS	Aorta	Aorta
40	chr1:150253800-150255600	Active TSS	Fetal Kidney	kidney
41	chr1:150253800-150255600	Active TSS	Ovary	ovary
42	chr1:150253800-150255600	Flanking Active TSS	Pancreas	Pancrea
43	chr1:150253800-150255600	Active TSS	Psoas Muscle	Psoas
44	chr1:150253800-150255600	Active TSS	NHLF	lung
45	chr1:150253800-150255800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:150253800-150255800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:150253800-150255800	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr1:150253800-150255800	Active TSS	Right Ventricle	heart
49	chr1:150253800-150256000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr1:150253800-150256000	Flanking Active TSS	Adipose Nuclei	Adipose

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