Variant report

Variant	rs10241107
Chromosome Location	chr7:100883973-100883974
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	UBTF	chr7:100883778-100884064	K562	blood:	n/a	n/a
2	MAX	chr7:100883699-100884002	K562	blood:	n/a	n/a
3	POLR2A	chr7:100881384-100884442	K562	blood:	n/a	n/a
4	POLR2A	chr7:100883719-100884199	K562	blood:	n/a	n/a
5	JUND	chr7:100883734-100884105	K562	blood:	n/a	n/a
6	CCNT2	chr7:100883740-100883992	K562	blood:	n/a	chr7:100883943-100883952 chr7:100883844-100883853
7	BHLHE40	chr7:100883928-100883992	K562	blood:	n/a	n/a
8	CBX3	chr7:100883686-100884100	K562	blood:	n/a	n/a
9	EGR1	chr7:100883640-100884101	K562	blood:	n/a	chr7:100883821-100883836 chr7:100883944-100883957
10	TBL1XR1	chr7:100883814-100884014	K562	blood:	n/a	n/a
11	USF1	chr7:100883573-100883994	K562	blood:	n/a	n/a
12	CHD2	chr7:100883816-100884027	K562	blood:	n/a	n/a
13	POLR2A	chr7:100883933-100884115	ProgFib	skin:	n/a	n/a
14	ZNF263	chr7:100883609-100884141	K562	blood:	n/a	chr7:100883807-100883816 chr7:100883937-100883946
15	RCOR1	chr7:100883730-100884112	K562	blood:	n/a	n/a
16	TEAD4	chr7:100883707-100884141	K562	blood:	n/a	n/a
17	HMGN3	chr7:100883762-100884030	K562	blood:	n/a	n/a
18	HCFC1	chr7:100883889-100884076	K562	blood:	n/a	n/a
19	ZNF263	chr7:100883845-100884041	HEK293-T-REx	kidney:	n/a	chr7:100883937-100883946
20	MAZ	chr7:100883646-100884145	K562	blood:	n/a	n/a
21	EGR1	chr7:100883628-100884063	K562	blood:	n/a	chr7:100883821-100883836 chr7:100883944-100883957
22	GATA1	chr7:100883510-100884559	PBDE	blood:	n/a	n/a
23	MAX	chr7:100883581-100884088	K562	blood:	n/a	n/a
24	ATF1	chr7:100883765-100884058	K562	blood:	n/a	n/a
25	NR2F2	chr7:100883541-100884270	K562	blood:	n/a	n/a
26	EP300	chr7:100883746-100884082	K562	blood:	n/a	chr7:100883824-100883837
27	POLR2A	chr7:100883549-100884561	PBDE	blood:	n/a	n/a
28	POLR2A	chr7:100883680-100884176	K562	blood:	n/a	n/a
29	MYC	chr7:100883731-100884006	K562	blood:	n/a	n/a
30	USF1	chr7:100883565-100884065	K562	blood:	n/a	n/a
31	POLR2A	chr7:100883395-100884152	K562	blood:	n/a	n/a
32	POLR2A	chr7:100883864-100884020	HepG2	liver:	n/a	n/a
33	ZBTB7A	chr7:100883608-100883993	K562	blood:	n/a	n/a
34	POLR2A	chr7:100883712-100884282	K562	blood:	n/a	n/a
35	ZBTB7A	chr7:100883523-100883997	K562	blood:	n/a	n/a
36	TAL1	chr7:100883787-100884023	K562	blood:	n/a	chr7:100883890-100883898
37	MYC	chr7:100883740-100884083	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100881101..100885645-chr7:100894081..100896862,4	MCF-7	breast:
2	chr7:100883935..100886693-chr7:100893948..100895706,3	K562	blood:
3	chr7:100883935..100885996-chr7:100893008..100895659,3	K562	blood:

Variant related genes	Relation type
CLDN15	TF binding region
ENSG00000214253	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10215699	1.00[EUR][1000 genomes]
rs10230367	0.86[EUR][1000 genomes]
rs10252307	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10254892	0.86[EUR][1000 genomes]
rs10255195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10257072	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10260707	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10260813	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10265206	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs10270498	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10273837	0.86[EUR][1000 genomes]
rs10487887	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12333955	0.95[EUR][1000 genomes]
rs12334190	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs28535695	0.86[EUR][1000 genomes]
rs28582264	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs28629340	0.86[EUR][1000 genomes]
rs28673822	0.84[EUR][1000 genomes]
rs28689891	0.86[EUR][1000 genomes]
rs56749963	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59554944	0.95[EUR][1000 genomes]
rs59937851	1.00[EUR][1000 genomes]
rs60536711	0.95[EUR][1000 genomes]
rs60719606	0.95[EUR][1000 genomes]
rs6946705	0.95[EUR][1000 genomes]
rs6946706	0.95[EUR][1000 genomes]
rs6947016	0.95[EUR][1000 genomes]
rs6947521	0.95[EUR][1000 genomes]
rs6947730	0.95[EUR][1000 genomes]
rs6957526	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6961873	0.95[EUR][1000 genomes]
rs6964812	1.00[EUR][1000 genomes]
rs6967483	0.87[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6975417	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6979122	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6979308	0.95[EUR][1000 genomes]
rs6979710	0.95[EUR][1000 genomes]
rs6979867	0.95[EUR][1000 genomes]
rs73713820	0.86[EUR][1000 genomes]
rs73713821	0.86[EUR][1000 genomes]
rs7778271	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7808669	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv534186	chr7:100773842-100898909	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv888818	chr7:100833153-100895480	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv607978	chr7:100861213-100971604	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv831077	chr7:100874209-101083930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10241107	CLDN15	cis	multi-tissue	Pritchard
rs10241107	FIS1	cis	Esophagus Muscularis	GTEx
rs10241107	FIS1	cis	lymphoblastoid	seeQTL
rs10241107	FIS1	cis	Adipose Subcutaneous	GTEx
rs10241107	FIS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10241107	FIS1	cis	Artery Tibial	GTEx
rs10241107	CLDN15	cis	Skin Sun Exposed Lower leg	GTEx
rs10241107	FIS1	cis	Artery Aorta	GTEx
rs10241107	CLDN15	Cis_1M	lymphoblastoid	RTeQTL
rs10241107	FIS1	cis	Whole Blood	GTEx
rs10241107	FIS1	cis	Thyroid	GTEx
rs10241107	FIS1	Cis_1M	lymphoblastoid	RTeQTL
rs10241107	CLDN15	cis	Artery Tibial	GTEx
rs10241107	FIS1	cis	multi-tissue	Pritchard
rs10241107	FIS1	cis	Esophagus Mucosa	GTEx
rs10241107	FIS1	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100862400-100887000	Weak transcription	Fetal Kidney	kidney
2	chr7:100863800-100884000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:100863800-100886800	Weak transcription	Psoas Muscle	Psoas
4	chr7:100863800-100886800	Weak transcription	Hela-S3	cervix
5	chr7:100865000-100884800	Strong transcription	Thymus	Thymus
6	chr7:100868400-100887600	Weak transcription	Small Intestine	intestine
7	chr7:100868800-100884200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:100876000-100887000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:100876200-100884400	Weak transcription	HMEC	breast
10	chr7:100876400-100887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:100876800-100886800	Weak transcription	Fetal Brain Male	brain
12	chr7:100877200-100884400	Strong transcription	Fetal Brain Female	brain
13	chr7:100877400-100884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:100878000-100884600	Genic enhancers	Spleen	Spleen
15	chr7:100878200-100884600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:100878200-100885000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:100878400-100884000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:100878400-100884400	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr7:100878600-100884800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:100878800-100884200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:100879000-100884200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:100879000-100884600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:100879200-100884400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:100879200-100884600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:100879600-100884600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:100879600-100884600	Strong transcription	Brain Germinal Matrix	brain
27	chr7:100879800-100884200	Strong transcription	Dnd41	blood
28	chr7:100880000-100884400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:100880200-100884600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:100880200-100884800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:100880200-100885600	Genic enhancers	Fetal Muscle Leg	muscle
32	chr7:100880400-100884200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:100880400-100884400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:100880400-100885600	Strong transcription	Aorta	Aorta
35	chr7:100880400-100885600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr7:100880600-100884000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:100880600-100884000	Genic enhancers	Pancreas	Pancrea
38	chr7:100880600-100884400	Strong transcription	Ovary	ovary
39	chr7:100880600-100884600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:100880600-100885600	Genic enhancers	Fetal Thymus	thymus
41	chr7:100880800-100887000	Genic enhancers	Placenta	Placenta
42	chr7:100881000-100884400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:100881400-100884200	Strong transcription	A549	lung
44	chr7:100881400-100884400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr7:100881400-100884400	Strong transcription	Brain Anterior Caudate	brain
46	chr7:100881400-100884400	Strong transcription	Osteobl	bone
47	chr7:100881600-100884400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr7:100881600-100884600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:100881600-100884800	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr7:100881800-100884400	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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