Variant report

Variant	rs6726833
Chromosome Location	chr2:39351569-39351570
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	TCF7L2	chr2:39351361-39351731	PANC-1	pancreas:	n/a	n/a
2	MAX	chr2:39350909-39352069	H1-hESC	embryonic stem cell:	n/a	chr2:39351384-39351394 chr2:39351634-39351644
3	CEBPB	chr2:39351557-39352167	MCF-7	breast:	n/a	chr2:39351872-39351883
4	CTCF	chr2:39351569-39351822	ProgFib	skin:	n/a	chr2:39351671-39351684 chr2:39351669-39351687 chr2:39351670-39351686 chr2:39351733-39351743 chr2:39351677-39351685
5	POLR2A	chr2:39350992-39351962	H1-neurons	neurons:	n/a	n/a
6	USF1	chr2:39351258-39351796	HepG2	liver:	n/a	n/a
7	USF1	chr2:39351275-39351846	SK-N-SH_RA	brain:	n/a	n/a
8	CEBPB	chr2:39351459-39351978	HepG2	liver:	n/a	chr2:39351872-39351883
9	TCF7L2	chr2:39350926-39352175	Hela-S3	cervix:	n/a	n/a
10	TAF7	chr2:39351045-39351696	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIX5	chr2:39351413-39351741	K562	blood:	n/a	n/a
12	CTCF	chr2:39351560-39351710	WI-38	lung:	n/a	chr2:39351671-39351684 chr2:39351669-39351687 chr2:39351670-39351686 chr2:39351677-39351685
13	MYC	chr2:39351506-39351750	MCF-7	breast:	n/a	chr2:39351634-39351644
14	E2F6	chr2:39350683-39351870	K562	blood:	n/a	chr2:39351466-39351475 chr2:39351640-39351649 chr2:39351702-39351709 chr2:39351489-39351500
15	RELA	chr2:39350831-39351972	GM15510	blood:	n/a	n/a
16	PML	chr2:39351060-39351839	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:39350894-39352230	K562	blood:	n/a	n/a
18	MAX	chr2:39350734-39351994	A549	lung:	n/a	chr2:39351384-39351394 chr2:39351634-39351644
19	EP300	chr2:39351421-39351806	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:39350829-39352215	ProgFib	skin:	n/a	n/a
21	MYC	chr2:39351213-39351811	MCF-7	breast:	n/a	chr2:39351384-39351394 chr2:39351634-39351644
22	TCF7L2	chr2:39351105-39351900	HCT-116	colon:	n/a	n/a
23	SIN3AK20	chr2:39351450-39351711	PFSK-1	brain:	n/a	n/a
24	EP300	chr2:39350879-39351904	A549	lung:	n/a	chr2:39351235-39351248
25	TCF3	chr2:39351304-39351854	GM12878	blood:	n/a	n/a
26	EP300	chr2:39351301-39351863	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr2:39351276-39352167	A549	lung:	n/a	chr2:39351872-39351883
28	MYC	chr2:39351525-39351778	GM12878	blood:	n/a	chr2:39351634-39351644
29	EP300	chr2:39351177-39351972	GM12878	blood:	n/a	chr2:39351235-39351248
30	NRF1	chr2:39350886-39352866	SK-N-SH	brain:	n/a	chr2:39351640-39351649 chr2:39351465-39351476 chr2:39351451-39351462 chr2:39351465-39351479 chr2:39351464-39351475
31	SRF	chr2:39351385-39351770	GM12878	blood:	n/a	n/a
32	HMGN3	chr2:39351299-39351890	K562	blood:	n/a	n/a
33	NFYB	chr2:39351301-39351640	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:39350640-39351963	PANC-1	pancreas:	n/a	n/a
35	CEBPB	chr2:39351182-39352116	MCF-7	breast:	n/a	chr2:39351872-39351883
36	USF1	chr2:39350900-39352112	A549	lung:	n/a	n/a
37	SRF	chr2:39351315-39351841	ECC-1	luminal epithelium:	n/a	n/a
38	MYC	chr2:39350966-39351870	K562	blood:	n/a	chr2:39351384-39351394 chr2:39351634-39351644
39	TCF12	chr2:39350957-39352022	ECC-1	luminal epithelium:	n/a	n/a
40	MAZ	chr2:39350946-39351959	HepG2	liver:	n/a	chr2:39351634-39351644
41	POLR2A	chr2:39350681-39352203	GM12892	blood:	n/a	n/a
42	CTCF	chr2:39351384-39351974	MCF-7	breast:	n/a	chr2:39351671-39351684 chr2:39351669-39351687 chr2:39351670-39351686 chr2:39351733-39351743 chr2:39351677-39351685
43	MYC	chr2:39351330-39351839	MCF10A-Er-Src	breast:	n/a	chr2:39351384-39351394 chr2:39351634-39351644
44	IRF1	chr2:39350911-39351918	K562	blood:	n/a	chr2:39351639-39351653
45	ELF1	chr2:39351163-39351831	MCF-7	breast:	n/a	n/a
46	CTCF	chr2:39351528-39351817	MCF-7	breast:	n/a	chr2:39351671-39351684 chr2:39351669-39351687 chr2:39351670-39351686 chr2:39351733-39351743 chr2:39351677-39351685
47	E2F4	chr2:39351004-39351894	K562	blood:	n/a	chr2:39351466-39351475 chr2:39351640-39351649 chr2:39351702-39351709
48	KAP1	chr2:39350952-39351940	U2OS	brain:	n/a	n/a
49	STAT5A	chr2:39350917-39352194	GM12878	blood:	n/a	chr2:39352019-39352031 chr2:39351642-39351654
50	REST	chr2:39351261-39351775	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:53895061..53895635-chr2:39351262..39351982,2	Hela-S3	cervix:
2	chr2:39351101..39351657-chr5:10249784..10250733,2	Hela-S3	cervix:
3	chr11:62439368..62440204-chr2:39351554..39352148,2	NB4	blood:
4	chr17:73149862..73150681-chr2:39351336..39351955,2	HCT-116	colon:
5	chr2:39350652..39354915-chr2:39355009..39358498,5	K562	blood:
6	chr2:39351098..39351964-chr2:113341975..113342944,2	NB4	blood:
7	chr11:33279534..33280463-chr2:39351094..39351986,2	Hela-S3	cervix:
8	chr2:39350652..39353712-chr2:39355009..39357216,3	K562	blood:
9	chr2:39351262..39352086-chr22:18121471..18121979,2	Hela-S3	cervix:
10	chr2:39350946..39351862-chr22:24109649..24110373,2	HCT-116	colon:
11	chr2:39348043..39352382-chr2:39450241..39456710,6	K562	blood:
12	chr17:39844940..39845521-chr2:39351175..39351784,2	Hela-S3	cervix:

Variant related genes	Relation type
SOS1	TF binding region
ENSG00000139546	Chromatin interaction
ENSG00000205111	Chromatin interaction
ENSG00000150756	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000202309	Chromatin interaction
ENSG00000099968	Chromatin interaction
ENSG00000110422	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000250479	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000150753	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10165968	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177250	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10184015	0.83[EUR][1000 genomes]
rs10190377	0.87[EUR][1000 genomes]
rs10200058	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11124660	0.84[EUR][1000 genomes]
rs12620003	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12620071	0.82[EUR][1000 genomes]
rs12622969	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031871	0.83[EUR][1000 genomes]
rs13033392	0.87[EUR][1000 genomes]
rs1377860	0.82[EUR][1000 genomes]
rs1377861	0.82[EUR][1000 genomes]
rs1377864	0.83[EUR][1000 genomes]
rs1454227	0.86[EUR][1000 genomes]
rs1470914	0.86[EUR][1000 genomes]
rs2060989	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123882	0.88[EUR][1000 genomes]
rs2168043	0.86[ASN][1000 genomes]
rs2924714	0.82[EUR][1000 genomes]
rs2969763	0.82[EUR][1000 genomes]
rs297120	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297121	0.82[EUR][1000 genomes]
rs297124	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs297125	0.82[EUR][1000 genomes]
rs297127	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297128	0.82[EUR][1000 genomes]
rs297129	0.82[EUR][1000 genomes]
rs297130	0.82[EUR][1000 genomes]
rs297131	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297132	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297133	0.82[EUR][1000 genomes]
rs297134	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297135	0.82[EUR][1000 genomes]
rs297136	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297137	0.82[EUR][1000 genomes]
rs297139	0.82[EUR][1000 genomes]
rs297140	0.82[EUR][1000 genomes]
rs297141	0.82[EUR][1000 genomes]
rs297142	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297143	0.82[EUR][1000 genomes]
rs297144	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297145	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297147	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297148	0.82[EUR][1000 genomes]
rs297149	0.82[EUR][1000 genomes]
rs297150	0.82[EUR][1000 genomes]
rs297151	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs297152	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs297153	0.82[EUR][1000 genomes]
rs297155	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297156	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297157	0.82[EUR][1000 genomes]
rs297158	0.84[EUR][1000 genomes]
rs297159	0.82[EUR][1000 genomes]
rs297161	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297162	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs366840	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs378698	0.82[EUR][1000 genomes]
rs3796038	0.86[EUR][1000 genomes]
rs388958	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4670905	0.82[EUR][1000 genomes]
rs57378308	0.84[EUR][1000 genomes]
rs59732351	0.84[EUR][1000 genomes]
rs61405040	0.82[EUR][1000 genomes]
rs6419600	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544191	0.82[EUR][1000 genomes]
rs6544197	0.82[EUR][1000 genomes]
rs72909662	0.84[EUR][1000 genomes]
rs970409	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6726833	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39350000-39352200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:39350000-39352600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:39350200-39352200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39350200-39352600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:39350400-39352200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:39350400-39352200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:39350400-39352400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:39350400-39352600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:39350400-39353000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:39350600-39352000	Active TSS	HSMM	muscle
11	chr2:39350600-39352200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:39350600-39352400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39350600-39352400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:39350600-39352800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:39350600-39352800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:39350800-39352200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:39350800-39352200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr2:39350800-39352400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:39350800-39352400	Active TSS	Esophagus	oesophagus
20	chr2:39350800-39352400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:39350800-39352600	Active TSS	Fetal Kidney	kidney
22	chr2:39350800-39352600	Active TSS	Right Atrium	heart
23	chr2:39350800-39352800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr2:39351000-39352000	Active TSS	Brain Anterior Caudate	brain
25	chr2:39351000-39352200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:39351000-39352200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:39351000-39352200	Active TSS	Colon Smooth Muscle	Colon
28	chr2:39351000-39352200	Active TSS	Gastric	stomach
29	chr2:39351000-39352400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:39351000-39352400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:39351000-39352400	Active TSS	Ovary	ovary
32	chr2:39351000-39352400	Active TSS	Small Intestine	intestine
33	chr2:39351000-39352400	Active TSS	NHDF-Ad	bronchial
34	chr2:39351000-39352600	Active TSS	Aorta	Aorta
35	chr2:39351200-39352000	Active TSS	Primary monocytes fromperipheralblood	blood
36	chr2:39351200-39352000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
37	chr2:39351200-39352000	Active TSS	Brain Hippocampus Middle	brain
38	chr2:39351200-39352000	Active TSS	Fetal Intestine Large	intestine
39	chr2:39351200-39352000	Active TSS	Fetal Intestine Small	intestine
40	chr2:39351200-39352000	Active TSS	Fetal Lung	lung
41	chr2:39351200-39352000	Active TSS	Placenta	Placenta
42	chr2:39351200-39352000	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:39351200-39352000	Active TSS	Spleen	Spleen
44	chr2:39351200-39352000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr2:39351200-39352000	Active TSS	Osteobl	bone
46	chr2:39351200-39352200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:39351200-39352200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:39351200-39352200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:39351200-39352200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:39351200-39352200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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