Variant report

Variant	rs2036844
Chromosome Location	chr5:126112153-126112154
allele	G/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	CEBPB	chr5:126111696-126112501	GM12878	blood:	n/a	chr5:126112256-126112273
2	MAX	chr5:126112044-126114710	HCT-116	colon:	n/a	n/a
3	POLR2A	chr5:126111728-126114531	PFSK-1	brain:	n/a	n/a
4	GATA3	chr5:126111973-126113276	A549	lung:	n/a	n/a
5	POLR2A	chr5:126111057-126115293	GM12878	blood:	n/a	n/a
6	ATF3	chr5:126112091-126112641	K562	blood:	n/a	n/a
7	POLR2A	chr5:126112099-126114877	GM12878	blood:	n/a	n/a
8	ELF1	chr5:126112011-126112883	MCF-7	breast:	n/a	n/a
9	RELA	chr5:126111991-126114834	GM15510	blood:	n/a	n/a
10	ZEB1	chr5:126112143-126112442	GM12878	blood:	n/a	n/a
11	MAX	chr5:126111958-126115083	NB4	blood:	n/a	chr5:126114904-126114913 chr5:126114903-126114913 chr5:126114903-126114914 chr5:126114905-126114912 chr5:126114902-126114915
12	CEBPD	chr5:126112039-126113599	K562	blood:	n/a	n/a
13	POLR2A	chr5:126111237-126115281	GM12891	blood:	n/a	n/a
14	POLR2A	chr5:126112037-126112758	GM12891	blood:	n/a	n/a
15	POLR2A	chr5:126112012-126114517	HUVEC	blood vessel:	n/a	n/a
16	E2F4	chr5:126112118-126114460	Hela-S3	cervix:	n/a	chr5:126114123-126114133 chr5:126114123-126114134 chr5:126114124-126114131 chr5:126112178-126112193 chr5:126114123-126114131 chr5:126114124-126114132 chr5:126114124-126114135 chr5:126113879-126113888 chr5:126114124-126114132
17	NFIC	chr5:126111055-126113198	GM12878	blood:	n/a	n/a
18	MAZ	chr5:126111857-126114511	IMR90	lung:	n/a	n/a
19	POLR2A	chr5:126111998-126114762	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:126111543-126115014	Hela-S3	cervix:	n/a	n/a
21	ATF3	chr5:126112142-126112730	A549	lung:	n/a	n/a
22	RELA	chr5:126111954-126113061	GM19099	blood:	n/a	n/a
23	ATF2	chr5:126111922-126113195	GM12878	blood:	n/a	chr5:126112262-126112269
24	POLR2A	chr5:126112075-126114546	H1-neurons	neurons:	n/a	n/a
25	MAFF	chr5:126111978-126112235	K562	blood:	n/a	n/a
26	RFX5	chr5:126112032-126114607	Hela-S3	cervix:	n/a	n/a
27	MYC	chr5:126112034-126113222	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr5:126112079-126114876	Hela-S3	cervix:	n/a	n/a
29	SP1	chr5:126112111-126112805	HepG2	liver:	n/a	chr5:126112791-126112802 chr5:126112766-126112777
30	STAT3	chr5:126111952-126112442	GM12878	blood:	n/a	chr5:126112400-126112411
31	GABPA	chr5:126112150-126112889	MCF-7	breast:	n/a	n/a
32	ATF1	chr5:126112091-126112779	K562	blood:	n/a	n/a
33	HDAC2	chr5:126111996-126112683	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:126111809-126115016	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr5:126112100-126114978	K562	blood:	n/a	chr5:126114904-126114913 chr5:126114903-126114913 chr5:126114903-126114914 chr5:126114905-126114912 chr5:126114902-126114915
36	NFYB	chr5:126111791-126112859	GM12878	blood:	n/a	chr5:126112686-126112701
37	CEBPB	chr5:126112004-126112731	MCF-7	breast:	n/a	chr5:126112256-126112273
38	MTA3	chr5:126111595-126113716	GM12878	blood:	n/a	n/a
39	RFX5	chr5:126112075-126112325	K562	blood:	n/a	n/a
40	SP1	chr5:126111933-126113049	A549	lung:	n/a	chr5:126112808-126112819 chr5:126112791-126112802 chr5:126112766-126112777
41	CREB1	chr5:126112077-126114480	HepG2	liver:	n/a	n/a
42	USF1	chr5:126112111-126112930	A549	lung:	n/a	n/a
43	PBX3	chr5:126112077-126112899	A549	lung:	n/a	n/a
44	ARID3A	chr5:126111877-126112488	K562	blood:	n/a	chr5:126112178-126112193
45	ZC3H11A	chr5:126112089-126112572	K562	blood:	n/a	n/a
46	RAD21	chr5:126112108-126112760	ECC-1	luminal epithelium:	n/a	n/a
47	MYBL2	chr5:126111959-126112973	HepG2	liver:	n/a	n/a
48	ZNF263	chr5:126111974-126114892	HEK293-T-REx	kidney:	n/a	n/a
49	TCF12	chr5:126112020-126112795	ECC-1	luminal epithelium:	n/a	n/a
50	ELK1	chr5:126112012-126112710	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126089250..126100296-chr5:126109758..126119075,20	K562	blood:
2	chr11:11863562..11864491-chr5:126112074..126112673,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCH3-1	chr5:126111987-126112178	ENSG00000251072.2

Variant related genes	Relation type
LMNB1	TF binding region
ENSG00000170242	Chromatin interaction
ENSG00000252185	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1510955	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271354	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941662	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941665	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941667	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973584	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2973585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973586	0.83[ASW][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2973593	0.81[MEX][hapmap]
rs2973599	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2973602	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2973603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2973888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973891	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973892	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62391737	0.82[ASN][1000 genomes]
rs6895856	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7729436	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2036844	SMARCD1	trans	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126111200-126112400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr5:126111200-126112400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:126111200-126112400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr5:126111200-126112600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:126111200-126112800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:126111200-126113400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:126111200-126113400	Active TSS	Fetal Brain Female	brain
8	chr5:126111200-126114400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:126111200-126114600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:126111200-126114600	Active TSS	NHLF	lung
11	chr5:126111200-126115000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:126111200-126115400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:126111200-126115800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:126111200-126115800	Active TSS	A549	lung
15	chr5:126111400-126112200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:126111400-126112200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr5:126111400-126112400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr5:126111400-126113000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:126111400-126113600	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr5:126111400-126114200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:126111400-126114400	Active TSS	Fetal Intestine Small	intestine
22	chr5:126111400-126114600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr5:126111400-126114800	Active TSS	NHDF-Ad	bronchial
24	chr5:126111400-126115000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:126111400-126115200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr5:126111400-126115200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr5:126111600-126112200	Flanking Active TSS	Liver	Liver
28	chr5:126111600-126112200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr5:126111600-126112200	Weak transcription	Pancreas	Pancrea
30	chr5:126111600-126112200	Flanking Active TSS	Dnd41	blood
31	chr5:126111600-126112400	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr5:126111600-126112400	Flanking Active TSS	NHEK	skin
33	chr5:126111600-126112600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr5:126111600-126113000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:126111600-126113000	Active TSS	HepG2	liver
36	chr5:126111600-126113200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:126111600-126113200	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr5:126111600-126113400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:126111600-126113800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:126111600-126114200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr5:126111600-126114400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr5:126111600-126114400	Active TSS	Fetal Lung	lung
43	chr5:126111600-126114400	Active TSS	HMEC	breast
44	chr5:126111600-126114400	Active TSS	HSMM	muscle
45	chr5:126111600-126114400	Active TSS	K562	blood
46	chr5:126111600-126114600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:126111600-126114600	Active TSS	Fetal Intestine Large	intestine
48	chr5:126111600-126114800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr5:126111600-126115000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr5:126111600-126116000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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