Variant report

Variant	rs71439230
Chromosome Location	chr2:38978078-38978079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:416)
CpG islands
(count:0)
Chromatin interactive
region (count:96)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:416 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB33	chr2:38977980-38978982	A549	lung:	n/a	n/a
2	ELF1	chr2:38977840-38978994	MCF-7	breast:	n/a	n/a
3	CEBPB	chr2:38978062-38978704	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr2:38977184-38979034	Hela-S3	cervix:	n/a	n/a
5	PAX5	chr2:38977813-38978900	GM12878	blood:	n/a	chr2:38977824-38977834
6	BHLHE40	chr2:38977775-38979011	HepG2	liver:	n/a	n/a
7	ATF3	chr2:38977652-38979017	A549	lung:	n/a	chr2:38978008-38978022
8	MAX	chr2:38977272-38978927	Hela-S3	cervix:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
9	CTCF	chr2:38977940-38978090	HBMEC	blood vessel:	n/a	n/a
10	YY1	chr2:38977865-38978712	GM12891	blood:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
11	MYC	chr2:38977986-38978750	MCF-7	breast:	n/a	chr2:38978721-38978731 chr2:38978724-38978734
12	NRF1	chr2:38977172-38978941	SK-N-SH	brain:	n/a	chr2:38978546-38978560 chr2:38978549-38978558 chr2:38978548-38978559 chr2:38978549-38978560
13	POLR2A	chr2:38977017-38979031	U87	brain:	n/a	n/a
14	CEBPB	chr2:38977783-38978877	K562	blood:	n/a	n/a
15	CREB1	chr2:38977750-38979113	K562	blood:	n/a	n/a
16	CEBPB	chr2:38978038-38979327	A549	lung:	n/a	n/a
17	TAF1	chr2:38977469-38979247	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr2:38977345-38979110	MCF-7	breast:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
19	MAX	chr2:38977092-38979186	HCT-116	colon:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
20	POLR2A	chr2:38976565-38978925	GM12878	blood:	n/a	n/a
21	MYC	chr2:38978020-38978715	Hela-S3	cervix:	n/a	n/a
22	ZEB1	chr2:38977924-38978752	GM12878	blood:	n/a	n/a
23	TAF1	chr2:38977523-38978914	HepG2	liver:	n/a	n/a
24	YY1	chr2:38977681-38979266	H1-hESC	embryonic stem cell:	n/a	chr2:38978041-38978049 chr2:38979179-38979190 chr2:38978218-38978232 chr2:38978259-38978269
25	NFATC1	chr2:38976771-38979006	GM12878	blood:	n/a	chr2:38978665-38978678
26	POLR2A	chr2:38969485-38979320	K562	blood:	n/a	n/a
27	CREB1	chr2:38977828-38978906	H1-hESC	embryonic stem cell:	n/a	n/a
28	HDAC2	chr2:38977126-38979047	HepG2	liver:	n/a	n/a
29	CREB1	chr2:38977773-38978948	K562	blood:	n/a	n/a
30	HMGN3	chr2:38977477-38978719	K562	blood:	n/a	n/a
31	NFIC	chr2:38977679-38978979	GM12878	blood:	n/a	n/a
32	EP300	chr2:38977866-38979047	ECC-1	luminal epithelium:	n/a	n/a
33	YY1	chr2:38977804-38978718	K562	blood:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
34	POLR2A	chr2:38977007-38979179	GM12892	blood:	n/a	n/a
35	PBX3	chr2:38977850-38979275	A549	lung:	n/a	n/a
36	FOXA2	chr2:38978052-38978923	A549	lung:	n/a	n/a
37	TAF1	chr2:38978076-38978806	MCF-7	breast:	n/a	n/a
38	MAFF	chr2:38977861-38979032	K562	blood:	n/a	n/a
39	SIN3AK20	chr2:38977107-38979159	MCF-7	breast:	n/a	n/a
40	POLR2A	chr2:38973829-38979359	H1-hESC	embryonic stem cell:	n/a	n/a
41	ATF2	chr2:38977705-38978983	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr2:38977381-38979087	SK-N-SH	brain:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
43	CHD2	chr2:38977439-38979002	GM12878	blood:	n/a	chr2:38977797-38977807
44	EP300	chr2:38977784-38978814	K562	blood:	n/a	n/a
45	POLR2A	chr2:38977284-38979369	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:38977274-38979095	GM19099	blood:	n/a	n/a
47	HEY1	chr2:38977375-38979369	HepG2	liver:	n/a	n/a
48	YY1	chr2:38977493-38978876	SK-N-SH_RA	brain:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
49	POLR2A	chr2:38977415-38978966	ProgFib	skin:	n/a	n/a
50	TCF7L2	chr2:38977762-38978932	PANC-1	pancreas:	n/a	n/a

No data

(count:96 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr2:38977870..38980067-chr2:42586942..42589703,3	K562	blood:
2	chr2:38694392..38697195-chr2:38976226..38979289,3	K562	blood:
3	chr2:38977833..38978509-chr6:146055931..146056536,2	Hela-S3	cervix:
4	chr2:38976823..38979247-chr4:785282..787385,2	MCF-7	breast:
5	chr2:38977712..38978642-chrX:134477790..134478766,2	Hela-S3	cervix:
6	chr1:145381301..145383000-chr2:38976945..38978478,2	MCF-7	breast:
7	chr13:115079612..115080161-chr2:38977967..38978630,2	Hela-S3	cervix:
8	chr14:75593386..75594157-chr2:38978042..38978637,2	Hela-S3	cervix:
9	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
10	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:
11	chr2:38976938..38979508-chr2:39454441..39457000,2	K562	blood:
12	chr2:38977645..38978510-chr5:41869545..41870347,2	Hela-S3	cervix:
13	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
14	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
15	chr2:38977967..38978942-chr2:70520501..70521308,2	Hela-S3	cervix:
16	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
17	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
18	chr13:53225264..53227638-chr2:38976930..38979242,2	MCF-7	breast:
19	chr2:38975187..38978600-chr2:39347007..39351369,4	K562	blood:
20	chr2:37457826..37459742-chr2:38976926..38979723,2	K562	blood:
21	chr2:38977519..38978087-chr7:891126..892040,2	Hela-S3	cervix:
22	chr2:38977028..38978558-chr3:149686195..149689135,2	MCF-7	breast:
23	chr2:38977980..38978897-chr2:122406649..122407552,2	NB4	blood:
24	chr19:5689960..5691696-chr2:38976849..38978490,2	K562	blood:
25	chr2:38695695..38697543-chr2:38977789..38979361,2	K562	blood:
26	chr1:152009033..152009552-chr2:38977795..38978319,2	Hela-S3	cervix:
27	chr2:38976891..38979056-chr2:39028521..39033921,5	MCF-7	breast:
28	chr1:241803496..241804225-chr2:38978064..38978860,2	HCT-116	colon:
29	chr1:36234620..36235540-chr2:38978035..38978956,2	Hela-S3	cervix:
30	chr2:38977935..38978503-chr6:27114641..27115435,2	Hela-S3	cervix:
31	chr2:38977031..38979396-chr2:85765814..85768332,2	K562	blood:
32	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
33	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
34	chr2:38976392..38979029-chr2:39027754..39033871,6	K562	blood:
35	chr12:122906977..122907658-chr2:38977576..38978525,2	Hela-S3	cervix:
36	chr1:28907913..28908555-chr2:38977671..38978692,3	Hela-S3	cervix:
37	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
38	chr18:77866823..77867548-chr2:38977208..38978100,2	Hela-S3	cervix:
39	chr14:31495712..31496510-chr2:38978077..38978584,2	Hela-S3	cervix:
40	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
41	chr11:61559555..61560111-chr2:38977912..38978564,2	Hela-S3	cervix:
42	chr2:38812622..38815204-chr2:38976239..38979096,3	K562	blood:
43	chr2:38977817..38978678-chr5:137667033..137667896,2	Hela-S3	cervix:
44	chr2:38601699..38605766-chr2:38977040..38979128,3	MCF-7	breast:
45	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:
46	chr2:38978045..38978827-chr4:41992165..41992826,2	Hela-S3	cervix:
47	chr12:120729525..120730218-chr2:38978025..38978704,2	Hela-S3	cervix:
48	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
49	chr1:182572923..182573893-chr2:38978049..38978657,2	Hela-S3	cervix:
50	chr2:38976661..38978798-chr2:39083252..39086476,5	MCF-7	breast:

No data

Variant related genes	Relation type
GEMIN6	TF binding region
SRSF7	TF binding region
ENSG00000120910	Chromatin interaction
ENSG00000120709	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000143333	Chromatin interaction
ENSG00000100345	Chromatin interaction
ENSG00000100221	Chromatin interaction
ENSG00000205111	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000196678	Chromatin interaction
ENSG00000119638	Chromatin interaction
ENSG00000198824	Chromatin interaction
ENSG00000138061	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000115944	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000153317	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000005189	Chromatin interaction
ENSG00000271443	Chromatin interaction
ENSG00000119787	Chromatin interaction
ENSG00000226445	Chromatin interaction
ENSG00000236859	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000164828	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000223922	Chromatin interaction
ENSG00000212628	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000168993	Chromatin interaction
ENSG00000150712	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000134825	Chromatin interaction
ENSG00000160746	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000129691	Chromatin interaction
ENSG00000198858	Chromatin interaction
ENSG00000090861	Chromatin interaction
ENSG00000207601	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000168496	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000232973	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000111640	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000118515	Chromatin interaction
ENSG00000100478	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000070087	Chromatin interaction
ENSG00000074054	Chromatin interaction
ENSG00000173275	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000120129	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000014824	Chromatin interaction
ENSG00000268175	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000158402	Chromatin interaction
ENSG00000248668	Chromatin interaction
ENSG00000214694	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000054277	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000259138	Chromatin interaction
ENSG00000231367	Chromatin interaction
ENSG00000101544	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000010626	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000186376	Chromatin interaction
ENSG00000143977	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000164898	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs13018921	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 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	chr2:38972600-38978400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:38973200-38978400	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr2:38973400-38978400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
4	chr2:38973800-38978400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr2:38975400-38978400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
6	chr2:38976200-38979000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:38976600-38978200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:38976600-38978600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:38976600-38978800	Active TSS	Pancreas	Pancrea
10	chr2:38976600-38978800	Active TSS	Stomach Mucosa	stomach
11	chr2:38976600-38979000	Active TSS	Ovary	ovary
12	chr2:38976600-38979200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:38976600-38979200	Active TSS	Psoas Muscle	Psoas
14	chr2:38976600-38979200	Active TSS	Right Ventricle	heart
15	chr2:38976600-38979400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:38976800-38978200	Active TSS	Right Atrium	heart
17	chr2:38976800-38978800	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:38976800-38978800	Active TSS	Fetal Muscle Trunk	muscle
19	chr2:38976800-38978800	Active TSS	Left Ventricle	heart
20	chr2:38976800-38978800	Active TSS	Lung	lung
21	chr2:38976800-38978800	Active TSS	HSMMtube	muscle
22	chr2:38976800-38979000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:38976800-38979000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:38976800-38979000	Active TSS	Aorta	Aorta
25	chr2:38976800-38979000	Active TSS	Fetal Heart	heart
26	chr2:38976800-38979000	Active TSS	Fetal Intestine Large	intestine
27	chr2:38976800-38979000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr2:38976800-38979000	Active TSS	Small Intestine	intestine
29	chr2:38976800-38979200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:38976800-38979200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr2:38976800-38979200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:38976800-38979200	Active TSS	Colon Smooth Muscle	Colon
33	chr2:38976800-38979600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:38977000-38978400	ZNF genes & repeats	Fetal Brain Male	brain
35	chr2:38977000-38978600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:38977000-38978800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:38977000-38978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:38977000-38978800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr2:38977000-38978800	Active TSS	Colonic Mucosa	Colon
40	chr2:38977000-38978800	Active TSS	Duodenum Mucosa	Duodenum
41	chr2:38977000-38978800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:38977000-38978800	Active TSS	Esophagus	oesophagus
43	chr2:38977000-38978800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr2:38977000-38978800	Active TSS	HUVEC	blood vessel
45	chr2:38977000-38979000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:38977000-38979000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:38977000-38979000	Active TSS	Fetal Intestine Small	intestine
48	chr2:38977000-38979400	Active TSS	Fetal Kidney	kidney
49	chr2:38977200-38978200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:38977200-38978400	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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