Variant report

Variant	rs3134628
Chromosome Location	chr2:38977612-38977613
allele	C/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	chr2:38977184-38979034	Hela-S3	cervix:	n/a	n/a
2	MAX	chr2:38977272-38978927	Hela-S3	cervix:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
3	NRF1	chr2:38977172-38978941	SK-N-SH	brain:	n/a	chr2:38978546-38978560 chr2:38978549-38978558 chr2:38978548-38978559 chr2:38978549-38978560
4	POLR2A	chr2:38977017-38979031	U87	brain:	n/a	n/a
5	TAF1	chr2:38977469-38979247	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr2:38977345-38979110	MCF-7	breast:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
7	MAX	chr2:38977092-38979186	HCT-116	colon:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
8	POLR2A	chr2:38976565-38978925	GM12878	blood:	n/a	n/a
9	TAF1	chr2:38977523-38978914	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:38977446-38977847	HUVEC	blood vessel:	n/a	n/a
11	NFATC1	chr2:38976771-38979006	GM12878	blood:	n/a	chr2:38978665-38978678
12	POLR2A	chr2:38969485-38979320	K562	blood:	n/a	n/a
13	HDAC2	chr2:38977126-38979047	HepG2	liver:	n/a	n/a
14	NRF1	chr2:38977321-38977628	GM12878	blood:	n/a	n/a
15	HMGN3	chr2:38977477-38978719	K562	blood:	n/a	n/a
16	POLR2A	chr2:38977007-38979179	GM12892	blood:	n/a	n/a
17	SIN3AK20	chr2:38977107-38979159	MCF-7	breast:	n/a	n/a
18	POLR2A	chr2:38973829-38979359	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr2:38977526-38977807	K562	blood:	n/a	n/a
20	YY1	chr2:38977381-38979087	SK-N-SH	brain:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
21	CHD2	chr2:38977439-38979002	GM12878	blood:	n/a	chr2:38977797-38977807
22	POLR2A	chr2:38977284-38979369	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:38977274-38979095	GM19099	blood:	n/a	n/a
24	HEY1	chr2:38977375-38979369	HepG2	liver:	n/a	n/a
25	YY1	chr2:38977493-38978876	SK-N-SH_RA	brain:	n/a	chr2:38978041-38978049 chr2:38978218-38978232 chr2:38978259-38978269
26	POLR2A	chr2:38977415-38978966	ProgFib	skin:	n/a	n/a
27	POLR2A	chr2:38973281-38979491	K562	blood:	n/a	n/a
28	CHD2	chr2:38977488-38979090	Hela-S3	cervix:	n/a	chr2:38977797-38977807
29	POLR2A	chr2:38977060-38979093	GM18505	blood:	n/a	n/a
30	MAX	chr2:38977337-38979049	SK-N-SH	brain:	n/a	chr2:38977600-38977609 chr2:38978721-38978731 chr2:38978724-38978734
31	SIN3A	chr2:38977380-38978864	GM12878	blood:	n/a	chr2:38978586-38978597
32	POLR2A	chr2:38977494-38979077	GM19193	blood:	n/a	n/a
33	CCNT2	chr2:38977488-38979006	K562	blood:	n/a	n/a
34	TAF7	chr2:38977587-38978690	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:38977477-38979095	NB4	blood:	n/a	n/a
36	MAX	chr2:38977498-38979448	HepG2	liver:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
37	MXI1	chr2:38977222-38978877	Hela-S3	cervix:	n/a	chr2:38978665-38978680
38	POU2F2	chr2:38977154-38978958	GM12878	blood:	n/a	chr2:38978219-38978231
39	POLR2A	chr2:38976569-38979156	GM12892	blood:	n/a	n/a
40	POLR2A	chr2:38977312-38978955	HEK293	kidney:	n/a	n/a
41	GTF2F1	chr2:38977151-38978980	K562	blood:	n/a	n/a
42	POLR2A	chr2:38977391-38979242	H1-neurons	neurons:	n/a	n/a
43	TBL1XR1	chr2:38976613-38979296	K562	blood:	n/a	n/a
44	MYC	chr2:38977326-38979642	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
45	CREB1	chr2:38977376-38979264	HepG2	liver:	n/a	n/a
46	PML	chr2:38976814-38979147	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:38977087-38979361	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:38976268-38979131	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr2:38977052-38979147	MCF10A-Er-Src	breast:	n/a	n/a
50	GATA3	chr2:38976887-38979203	A549	lung:	n/a	chr2:38978735-38978746 chr2:38978927-38978934 chr2:38976996-38977007

No.	Distal block	Cell Line	Cell type
1	chr2:38694392..38697195-chr2:38976226..38979289,3	K562	blood:
2	chr2:38976823..38979247-chr4:785282..787385,2	MCF-7	breast:
3	chr15:72409880..72410484-chr2:38976828..38977720,2	Hela-S3	cervix:
4	chr1:145381301..145383000-chr2:38976945..38978478,2	MCF-7	breast:
5	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
6	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:
7	chr2:38976938..38979508-chr2:39454441..39457000,2	K562	blood:
8	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
9	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
10	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
11	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
12	chr13:53225264..53227638-chr2:38976930..38979242,2	MCF-7	breast:
13	chr2:38975187..38978600-chr2:39347007..39351369,4	K562	blood:
14	chr2:37457826..37459742-chr2:38976926..38979723,2	K562	blood:
15	chr2:38977519..38978087-chr7:891126..892040,2	Hela-S3	cervix:
16	chr2:38977028..38978558-chr3:149686195..149689135,2	MCF-7	breast:
17	chr19:5689960..5691696-chr2:38976849..38978490,2	K562	blood:
18	chr2:38976891..38979056-chr2:39028521..39033921,5	MCF-7	breast:
19	chr2:38977031..38979396-chr2:85765814..85768332,2	K562	blood:
20	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
21	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
22	chr2:38976392..38979029-chr2:39027754..39033871,6	K562	blood:
23	chr12:122906977..122907658-chr2:38977576..38978525,2	Hela-S3	cervix:
24	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
25	chr18:77866823..77867548-chr2:38977208..38978100,2	Hela-S3	cervix:
26	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
27	chr2:38812622..38815204-chr2:38976239..38979096,3	K562	blood:
28	chr2:38601699..38605766-chr2:38977040..38979128,3	MCF-7	breast:
29	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:
30	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
31	chr2:38976661..38978798-chr2:39083252..39086476,5	MCF-7	breast:
32	chr2:38976457..38978515-chr2:39347011..39349138,2	K562	blood:
33	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
34	chr2:38975535..38978590-chr2:39035789..39038871,3	MCF-7	breast:
35	chr2:38602255..38605343-chr2:38976114..38979530,4	K562	blood:
36	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
37	chr2:38977082..38978650-chr2:39037995..39040389,2	K562	blood:
38	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:
39	chr2:38977033..38979904-chr2:47402717..47404547,2	K562	blood:
40	chr2:38892007..38895113-chr2:38976994..38979857,4	K562	blood:
41	chr2:38300805..38303904-chr2:38976182..38979449,4	MCF-7	breast:
42	chr12:7012428..7015040-chr2:38976959..38979555,2	K562	blood:
43	chr2:38742460..38744108-chr2:38976998..38978688,2	MCF-7	breast:
44	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
45	chr2:38977053..38978639-chr7:120723003..120724994,2	K562	blood:
46	chr2:38977319..38978523-chr5:32312613..32313523,3	Hela-S3	cervix:
47	chr2:38602430..38604455-chr2:38976753..38978503,3	K562	blood:
48	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
49	chr1:27191158..27192083-chr2:38977218..38978092,2	Hela-S3	cervix:
50	chr19:912428..913396-chr2:38977509..38978848,3	Hela-S3	cervix:

Variant related genes	Relation type
GEMIN6	TF binding region
SRSF7	TF binding region
ENSG00000066933	Chromatin interaction
ENSG00000205111	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000231367	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000223922	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000150712	Chromatin interaction
ENSG00000198858	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000271443	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000212628	Chromatin interaction
ENSG00000268175	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000138061	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000101544	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000164828	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000070087	Chromatin interaction
ENSG00000119787	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000232973	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000168993	Chromatin interaction
ENSG00000010626	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10197412	1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[ASN][1000 genomes]
rs10865143	0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[ASN][1000 genomes]
rs11124646	0.84[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11898812	0.83[CHB][hapmap]
rs12472454	0.92[ASN][1000 genomes]
rs12474770	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618118	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs12621103	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12991609	0.82[ASN][1000 genomes]
rs13024811	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979143	0.82[CHD][hapmap]
rs2037875	1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[ASN][1000 genomes]
rs3097713	0.80[ASW][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs3097714	0.88[CHD][hapmap]
rs3099952	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3099960	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3099961	0.86[ASN][1000 genomes]
rs3099965	0.84[ASN][1000 genomes]
rs3099968	0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[ASN][1000 genomes]
rs3099971	0.89[ASN][1000 genomes]
rs3112183	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112184	0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs3112186	0.89[ASN][1000 genomes]
rs3112188	0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs3112189	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112191	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112192	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112194	0.85[ASN][1000 genomes]
rs3112196	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs3112198	0.88[ASN][1000 genomes]
rs3112200	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs3112204	0.86[ASN][1000 genomes]
rs3112209	0.80[EUR][1000 genomes]
rs3112215	0.88[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs3134629	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134630	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134637	0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35387882	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731838	0.85[CHD][hapmap]
rs4670892	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670894	0.84[EUR][1000 genomes]
rs6715866	0.94[CHD][hapmap];0.94[GIH][hapmap];0.83[ASN][1000 genomes]
rs6717670	0.83[CHB][hapmap]

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	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
4	esv1834132	chr2:38955977-38977612	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	43 gene(s)	inside rSNPs	diseases
5	esv1836070	chr2:38955977-38977612	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3134628	MORN2	cis	cerebellum	SCAN
rs3134628	DHX57	cis	cerebellum	SCAN
rs3134628	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38972600-38978400	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	chr2:38976800-38978000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr2:38976800-38978200	Active TSS	Right Atrium	heart
18	chr2:38976800-38978800	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:38976800-38978800	Active TSS	Fetal Muscle Trunk	muscle
20	chr2:38976800-38978800	Active TSS	Left Ventricle	heart
21	chr2:38976800-38978800	Active TSS	Lung	lung
22	chr2:38976800-38978800	Active TSS	HSMMtube	muscle
23	chr2:38976800-38979000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:38976800-38979000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:38976800-38979000	Active TSS	Aorta	Aorta
26	chr2:38976800-38979000	Active TSS	Fetal Heart	heart
27	chr2:38976800-38979000	Active TSS	Fetal Intestine Large	intestine
28	chr2:38976800-38979000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr2:38976800-38979000	Active TSS	Small Intestine	intestine
30	chr2:38976800-38979200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:38976800-38979200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:38976800-38979200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:38976800-38979200	Active TSS	Colon Smooth Muscle	Colon
34	chr2:38976800-38979600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr2:38977000-38977800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr2:38977000-38978400	ZNF genes & repeats	Fetal Brain Male	brain
37	chr2:38977000-38978600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:38977000-38978800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:38977000-38978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:38977000-38978800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr2:38977000-38978800	Active TSS	Colonic Mucosa	Colon
42	chr2:38977000-38978800	Active TSS	Duodenum Mucosa	Duodenum
43	chr2:38977000-38978800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr2:38977000-38978800	Active TSS	Esophagus	oesophagus
45	chr2:38977000-38978800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:38977000-38978800	Active TSS	HUVEC	blood vessel
47	chr2:38977000-38979000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:38977000-38979000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:38977000-38979000	Active TSS	Fetal Intestine Small	intestine
50	chr2:38977000-38979400	Active TSS	Fetal Kidney	kidney

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