Variant report

Variant	rs17641133
Chromosome Location	chr3:53878597-53878598
allele	A/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	chr3:53878328-53878834	HepG2	liver:	n/a	n/a
2	MBD4	chr3:53878488-53879580	HepG2	liver:	n/a	n/a
3	HEY1	chr3:53876036-53880070	HepG2	liver:	n/a	n/a
4	HEY1	chr3:53876129-53880020	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:53877216-53879627	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:53876086-53880024	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:53876459-53880951	HepG2	liver:	n/a	n/a
8	HNF4A	chr3:53878265-53879351	HepG2	liver:	n/a	chr3:53878890-53878902 chr3:53878888-53878903 chr3:53878888-53878903 chr3:53879036-53879050 chr3:53878888-53878901 chr3:53878889-53878901 chr3:53878888-53878903 chr3:53878447-53878462 chr3:53878889-53878901 chr3:53878888-53878903 chr3:53878886-53878904 chr3:53878889-53878902 chr3:53879037-53879049 chr3:53878888-53878902 chr3:53878889-53878901 chr3:53879037-53879050 chr3:53878889-53878901 chr3:53878888-53878902
9	MAX	chr3:53878462-53878613	GM12878	blood:	n/a	chr3:53878578-53878587
10	POLR2A	chr3:53875240-53880984	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:53876725-53878869	GM19099	blood:	n/a	n/a
12	POLR2A	chr3:53877904-53881035	GM19193	blood:	n/a	n/a
13	POLR2A	chr3:53877360-53880992	GM18951	blood:	n/a	n/a
14	EBF1	chr3:53876510-53878643	GM12878	blood:	n/a	chr3:53878322-53878332 chr3:53877615-53877624 chr3:53877975-53877986 chr3:53878323-53878332
15	MYC	chr3:53878512-53878645	HepG2	liver:	n/a	chr3:53878578-53878587
16	TAF1	chr3:53878057-53879395	HepG2	liver:	n/a	n/a
17	HNF4A	chr3:53878384-53879271	HepG2	liver:	n/a	chr3:53878890-53878902 chr3:53878888-53878903 chr3:53878888-53878903 chr3:53879036-53879050 chr3:53878888-53878901 chr3:53878889-53878901 chr3:53878888-53878903 chr3:53878447-53878462 chr3:53878889-53878901 chr3:53878888-53878903 chr3:53878886-53878904 chr3:53878889-53878902 chr3:53879037-53879049 chr3:53878888-53878902 chr3:53878889-53878901 chr3:53879037-53879050 chr3:53878889-53878901 chr3:53878888-53878902
18	NFIC	chr3:53878444-53879232	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:53876293-53881852	HepG2	liver:	n/a	n/a
20	MAFF	chr3:53878556-53879154	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:53876116-53879632	HepG2	liver:	n/a	n/a
22	YY1	chr3:53878591-53879196	HepG2	liver:	n/a	n/a
23	MYBL2	chr3:53878313-53879708	HepG2	liver:	n/a	n/a
24	TBP	chr3:53876673-53879496	HepG2	liver:	n/a	n/a
25	WRNIP1	chr3:53878474-53878744	GM12878	blood:	n/a	n/a
26	MYBL2	chr3:53878424-53879371	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:53876680-53880844	GM12891	blood:	n/a	n/a
28	RFX5	chr3:53878396-53879539	HepG2	liver:	n/a	n/a
29	MAFK	chr3:53878504-53879097	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:53876430-53879414	HepG2	liver:	n/a	n/a
31	YY1	chr3:53878407-53879407	HepG2	liver:	n/a	n/a
32	MAX	chr3:53876250-53881108	HepG2	liver:	n/a	chr3:53878578-53878587
33	JUND	chr3:53878431-53878718	HepG2	liver:	n/a	chr3:53878578-53878586 chr3:53878576-53878587 chr3:53878576-53878588 chr3:53878576-53878587
34	POLR2A	chr3:53876647-53879870	HepG2	liver:	n/a	n/a
35	RCOR1	chr3:53878462-53879692	HepG2	liver:	n/a	n/a
36	NFIC	chr3:53878436-53879205	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53874777..53878635-chr3:53878874..53882397,7	MCF-7	breast:

Variant related genes	Relation type
IL17RB	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1025690	0.92[EUR][1000 genomes]
rs10510765	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10510766	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11705918	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11706303	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11708227	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11709505	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11719179	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13075639	1.00[ASN][1000 genomes]
rs13076366	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13082692	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13092344	1.00[ASN][1000 genomes]
rs17053338	1.00[CHB][hapmap]
rs17053532	1.00[ASN][1000 genomes]
rs2118421	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125876	1.00[ASN][1000 genomes]
rs2232333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276839	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2289205	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2359204	1.00[ASN][1000 genomes]
rs2633726	1.00[ASN][1000 genomes]
rs28675949	1.00[ASN][1000 genomes]
rs35377175	1.00[ASN][1000 genomes]
rs35414202	1.00[ASN][1000 genomes]
rs35657034	1.00[ASN][1000 genomes]
rs3755817	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4453827	1.00[ASN][1000 genomes]
rs4546140	0.90[EUR][1000 genomes]
rs45560831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45616236	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687586	1.00[CHB][hapmap]
rs55974100	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56052250	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445606	1.00[CHB][hapmap]
rs73092085	1.00[ASN][1000 genomes]
rs893363	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17641133	CHDH	cis	Nerve Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:53856800-53879200	Weak transcription	Ovary	ovary
5	chr3:53865600-53879800	Weak transcription	Aorta	Aorta
6	chr3:53869600-53879600	Weak transcription	Right Atrium	heart
7	chr3:53870200-53878600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:53870800-53879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:53875200-53878600	Enhancers	Stomach Mucosa	stomach
10	chr3:53875200-53879200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:53875200-53879400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:53875400-53878600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:53875400-53878800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:53875600-53879000	Enhancers	Fetal Intestine Small	intestine
15	chr3:53875600-53879200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:53875600-53879200	Enhancers	Brain Anterior Caudate	brain
17	chr3:53876200-53878600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:53876200-53878600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:53876200-53879200	Enhancers	Brain Angular Gyrus	brain
20	chr3:53876200-53879600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:53876400-53878800	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:53876400-53878800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:53876400-53879000	Enhancers	Brain Substantia Nigra	brain
24	chr3:53876400-53879200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:53876400-53879200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:53876400-53879200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:53876400-53879200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:53876400-53879400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:53876600-53879600	Enhancers	Lung	lung
30	chr3:53876800-53879200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:53877000-53879400	Weak transcription	Fetal Kidney	kidney
32	chr3:53877200-53879200	Enhancers	Colonic Mucosa	Colon
33	chr3:53877400-53879400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:53877400-53879800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:53877600-53878600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:53877600-53878600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:53877600-53878800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:53877600-53878800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:53877600-53878800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:53877600-53878800	Weak transcription	HMEC	breast
41	chr3:53877600-53879400	Weak transcription	Right Ventricle	heart
42	chr3:53877600-53879600	Weak transcription	Spleen	Spleen
43	chr3:53877600-53879800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:53877800-53879000	Weak transcription	A549	lung
45	chr3:53878000-53879400	Flanking Active TSS	Liver	Liver
46	chr3:53878000-53879400	Enhancers	Small Intestine	intestine
47	chr3:53878000-53879600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr3:53878000-53879800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:53878000-53880200	Active TSS	Stomach Smooth Muscle	stomach
50	chr3:53878200-53878600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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