Variant report

Variant	rs221801
Chromosome Location	chr7:100290031-100290032
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	POLR2A	chr7:100289336-100290218	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:100289223-100290189	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:100289103-100290163	K562	blood:	n/a	n/a
4	POLR2A	chr7:100289193-100290326	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr7:100289964-100290207	K562	blood:	n/a	n/a
6	IKZF1	chr7:100289708-100290084	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:100289347-100290739	K562	blood:	n/a	n/a
8	ZNF263	chr7:100289362-100290271	HEK293-T-REx	kidney:	n/a	chr7:100290166-100290175 chr7:100289554-100289575
9	SMC3	chr7:100288186-100291400	SK-N-SH	brain:	n/a	chr7:100289216-100289230 chr7:100288446-100288456 chr7:100289506-100289516 chr7:100289447-100289457 chr7:100289447-100289461
10	HEY1	chr7:100289378-100290143	K562	blood:	n/a	n/a
11	POLR2A	chr7:100288369-100290133	K562	blood:	n/a	n/a
12	MAX	chr7:100289894-100290087	K562	blood:	n/a	n/a
13	RAD21	chr7:100288338-100290934	SK-N-SH	brain:	n/a	chr7:100289443-100289462 chr7:100288871-100288883 chr7:100289480-100289493 chr7:100289445-100289457 chr7:100290681-100290690 chr7:100288444-100288456 chr7:100289447-100289457 chr7:100289242-100289252 chr7:100288446-100288456 chr7:100289240-100289252
14	TEAD4	chr7:100289287-100290485	K562	blood:	n/a	n/a
15	MAZ	chr7:100288815-100290746	IMR90	lung:	n/a	chr7:100290341-100290350 chr7:100290337-100290352 chr7:100289322-100289332 chr7:100290340-100290351 chr7:100290340-100290351 chr7:100289224-100289234 chr7:100290340-100290351
16	POLR2A	chr7:100289103-100291438	SK-N-MC	brain:	n/a	n/a
17	MAX	chr7:100289218-100290870	K562	blood:	n/a	chr7:100290341-100290350 chr7:100290337-100290352 chr7:100290315-100290325 chr7:100289322-100289332 chr7:100290340-100290351 chr7:100290340-100290351 chr7:100289224-100289234 chr7:100290340-100290351
18	TEAD4	chr7:100289234-100290813	K562	blood:	n/a	n/a
19	MYC	chr7:100290020-100290520	K562	blood:	n/a	chr7:100290341-100290350 chr7:100290337-100290352 chr7:100290315-100290325 chr7:100290340-100290351 chr7:100290340-100290351 chr7:100290340-100290351
20	CTCF	chr7:100288330-100291509	SK-N-SH	brain:	n/a	chr7:100289445-100289463 chr7:100289242-100289255 chr7:100289447-100289460 chr7:100291304-100291317 chr7:100289217-100289230 chr7:100288748-100288756 chr7:100289440-100289461
21	WRNIP1	chr7:100289488-100290159	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:100289139-100290039	K562	blood:	n/a	n/a
23	POLR2A	chr7:100290014-100290093	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100289314..100293442-chr7:100296051..100298941,4	MCF-7	breast:
2	chr7:100025163..100029050-chr7:100284721..100290800,5	MCF-7	breast:
3	chr7:100068696..100070699-chr7:100288610..100291361,2	MCF-7	breast:
4	chr7:100144116..100146517-chr7:100289943..100291876,2	K562	blood:
5	chr7:100184159..100186286-chr7:100289610..100292155,2	MCF-7	breast:
6	chr7:100288321..100291208-chr7:100293573..100296644,3	K562	blood:
7	chr7:100222794..100225924-chr7:100289657..100292852,4	MCF-7	breast:
8	chr7:100182628..100184656-chr7:100289002..100291163,2	K562	blood:
9	chr7:100066617..100067553-chr7:100289383..100290035,2	K562	blood:
10	chr7:100288992..100293891-chr7:100317292..100321001,4	MCF-7	breast:
11	chr7:100199658..100204753-chr7:100287607..100293733,10	K562	blood:
12	chr7:100289903..100293307-chr7:100301970..100305114,7	K562	blood:
13	chr7:100288252..100292867-chr7:100319528..100322364,4	K562	blood:
14	chr7:100199953..100202324-chr7:100288023..100291009,2	MCF-7	breast:
15	chr7:100287688..100293699-chr7:100300603..100306359,15	MCF-7	breast:
16	chr7:100031056..100033045-chr7:100289882..100292059,2	K562	blood:
17	chr7:100162910..100168606-chr7:100287546..100292436,6	MCF-7	breast:
18	chr7:100198433..100204411-chr7:100285757..100293733,14	K562	blood:
19	chr7:100222173..100224759-chr7:100289298..100291069,2	K562	blood:
20	chr7:100239190..100240878-chr7:100289804..100292344,2	MCF-7	breast:
21	chr7:100289903..100293628-chr7:100299918..100304988,11	K562	blood:
22	chr7:100208850..100211238-chr7:100289549..100292875,4	K562	blood:
23	chr7:100289891..100291847-chr7:100416190..100417802,2	K562	blood:
24	chr7:100197481..100201934-chr7:100289981..100293981,6	MCF-7	breast:
25	chr7:100025861..100030068-chr7:100288797..100293203,7	K562	blood:
26	chr7:100181942..100185382-chr7:100289663..100293010,6	K562	blood:
27	chr7:100288932..100290679-chr7:100483688..100485716,2	K562	blood:
28	chr7:100180869..100184882-chr7:100287482..100291355,9	MCF-7	breast:
29	chr7:100025034..100028922-chr7:100288914..100292951,6	K562	blood:
30	chr7:100207033..100212293-chr7:100287661..100294075,8	MCF-7	breast:
31	chr7:100034415..100037250-chr7:100289483..100291820,2	MCF-7	breast:
32	chr7:100027286..100029611-chr7:100288264..100290842,2	MCF-7	breast:
33	chr7:100179120..100183907-chr7:100289595..100293366,6	MCF-7	breast:
34	chr7:100288390..100292044-chr7:100484527..100487788,3	MCF-7	breast:

Variant related genes	Relation type
GIGYF1	TF binding region
ENSG00000224729	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000184414	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000130427	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10277087	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10953301	0.89[JPT][hapmap]
rs11520986	0.89[JPT][hapmap]
rs11974395	0.89[JPT][hapmap]
rs11979818	0.89[JPT][hapmap]
rs11983334	0.89[JPT][hapmap]
rs1617640	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[EUR][1000 genomes]
rs1734908	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1734909	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1734910	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075672	0.82[MEX][hapmap]
rs221771	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221772	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221788	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221795	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2272572	0.89[JPT][hapmap]
rs2432930	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727459	0.89[JPT][hapmap]
rs4729597	0.83[MEX][hapmap]
rs4729602	0.89[JPT][hapmap]
rs4729606	0.89[JPT][hapmap]
rs4729607	0.89[JPT][hapmap]
rs475339	0.92[EUR][1000 genomes]
rs504141	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs507392	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[EUR][1000 genomes]
rs551238	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs554055	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs568733	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs576236	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh 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	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888795	chr7:100266081-100298626	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs221801	MOSPD3	cis	Whole Blood	GTEx
rs221801	TSC22D4	cis	parietal	SCAN
rs221801	DLX5	cis	cerebellum	SCAN
rs221801	C10orf107	trans	parietal	SCAN
rs221801	PILRB	cis	cerebellum	SCAN
rs221801	MEPCE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100274200-100290400	Weak transcription	HSMMtube	muscle
2	chr7:100281600-100290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:100284000-100290400	Weak transcription	Small Intestine	intestine
4	chr7:100285800-100290600	Weak transcription	Aorta	Aorta
5	chr7:100287200-100290400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr7:100287800-100290200	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:100287800-100290800	Enhancers	Liver	Liver
8	chr7:100288400-100290200	Enhancers	Psoas Muscle	Psoas
9	chr7:100288400-100290400	Enhancers	Placenta	Placenta
10	chr7:100288400-100290600	Enhancers	Pancreas	Pancrea
11	chr7:100288400-100290800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:100288600-100290400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:100288600-100290400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:100288600-100290800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr7:100288600-100290800	Flanking Active TSS	HepG2	liver
16	chr7:100288600-100291200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr7:100288800-100290200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:100288800-100290400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr7:100288800-100290400	Enhancers	Stomach Mucosa	stomach
20	chr7:100288800-100290600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr7:100288800-100290600	Enhancers	Left Ventricle	heart
22	chr7:100288800-100290800	Flanking Active TSS	Fetal Brain Female	brain
23	chr7:100288800-100290800	Enhancers	Gastric	stomach
24	chr7:100288800-100290800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr7:100288800-100290800	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr7:100288800-100291000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:100288800-100291000	Enhancers	Spleen	Spleen
28	chr7:100289000-100290600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr7:100289000-100290800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:100289000-100290800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:100289000-100290800	Enhancers	Primary B cells from peripheral blood	blood
32	chr7:100289000-100290800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:100289000-100290800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:100289200-100290400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:100289200-100290400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:100289200-100290400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:100289200-100290800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:100289200-100290800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr7:100289200-100290800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:100289200-100290800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:100289200-100290800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr7:100289200-100290800	Flanking Active TSS	Thymus	Thymus
43	chr7:100289200-100290800	Flanking Active TSS	NHLF	lung
44	chr7:100289200-100291000	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr7:100289200-100291000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:100289200-100291200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:100289400-100290200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
48	chr7:100289400-100290600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
49	chr7:100289400-100290600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:100289400-100290800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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