Variant report

Variant	rs7978
Chromosome Location	chr16:74486189-74486190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr16:74486034-74486776	GM12878	blood:	n/a	n/a
2	FOXM1	chr16:74486101-74486701	GM12878	blood:	n/a	n/a
3	RUNX3	chr16:74486139-74486711	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:74486121-74486209	H1-hESC	embryonic stem cell:	n/a	n/a
5	PAX5	chr16:74486017-74486676	GM12878	blood:	n/a	n/a
6	NFATC1	chr16:74486115-74486658	GM12878	blood:	n/a	n/a
7	ATF2	chr16:74486087-74486651	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:74486076-74486567	GM12878	blood:	n/a	n/a
9	RUNX3	chr16:74486086-74486728	GM12878	blood:	n/a	n/a
10	POLR2A	chr16:74485926-74486623	GM12892	blood:	n/a	n/a
11	PML	chr16:74486066-74486659	GM12878	blood:	n/a	n/a
12	PAX5	chr16:74486069-74486571	GM12892	blood:	n/a	n/a
13	RELA	chr16:74486174-74486614	GM18951	blood:	n/a	n/a
14	ELF1	chr16:74486079-74486564	GM12878	blood:	n/a	n/a
15	POU2F2	chr16:74485999-74486617	GM12891	blood:	n/a	n/a
16	NFATC1	chr16:74486185-74486629	GM12878	blood:	n/a	n/a
17	STAT5A	chr16:74486140-74486621	GM12878	blood:	n/a	n/a
18	ELF1	chr16:74485964-74486633	GM12878	blood:	n/a	n/a
19	PAX5	chr16:74486179-74486548	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:74486059-74486323	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr16:74485785-74486638	GM12878	blood:	n/a	n/a
22	CEBPB	chr16:74486088-74486642	GM12878	blood:	n/a	n/a
23	PAX5	chr16:74486132-74486609	GM12878	blood:	n/a	n/a
24	FOS	chr16:74485843-74486228	HUVEC	blood vessel:	n/a	n/a
25	TCF3	chr16:74486120-74486522	GM12878	blood:	n/a	n/a
26	PAX5	chr16:74486055-74486644	GM12891	blood:	n/a	n/a
27	RCOR1	chr16:74486143-74486539	GM12878	blood:	n/a	n/a
28	PAX5	chr16:74486135-74486562	GM12878	blood:	n/a	n/a
29	NFIC	chr16:74485936-74486653	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr16:74486171-74486577	GM12878	blood:	n/a	n/a
31	NFIC	chr16:74486130-74486696	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74483167..74486389-chr16:74491599..74494939,3	MCF-7	breast:
2	chr16:74484871..74487119-chr16:74488063..74490451,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260539	TF binding region
RNU6-237P	TF binding region
ENSG00000090863	Chromatin interaction
ENSG00000251794	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1019572	0.86[JPT][hapmap];0.91[YRI][hapmap]
rs1019573	0.86[JPT][hapmap];0.91[YRI][hapmap]
rs10500587	0.86[JPT][hapmap]
rs11149722	0.92[JPT][hapmap];0.86[YRI][hapmap]
rs1132843	0.84[AFR][1000 genomes]
rs11639812	0.92[JPT][hapmap];0.90[YRI][hapmap]
rs11644298	0.92[JPT][hapmap]
rs11648868	0.92[JPT][hapmap]
rs12325017	0.92[JPT][hapmap];0.90[YRI][hapmap]
rs12446054	0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs12448026	0.85[JPT][hapmap]
rs12598701	0.86[JPT][hapmap]
rs13339161	0.92[JPT][hapmap]
rs13359	0.92[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs1469140	0.92[JPT][hapmap]
rs2098754	0.92[JPT][hapmap]
rs2288053	0.92[JPT][hapmap];0.90[YRI][hapmap]
rs2303275	0.92[JPT][hapmap]
rs2303278	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs2303281	0.92[JPT][hapmap]
rs3785312	0.86[JPT][hapmap];0.91[YRI][hapmap]
rs3826239	0.92[JPT][hapmap];0.90[YRI][hapmap]
rs3851729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851730	0.91[AFR][1000 genomes]
rs4438331	0.85[JPT][hapmap]
rs4887772	0.92[JPT][hapmap]
rs4887776	0.85[JPT][hapmap]
rs4887777	0.85[JPT][hapmap]
rs4887779	0.85[JPT][hapmap]
rs4888238	0.92[JPT][hapmap];0.82[YRI][hapmap]
rs4888240	0.85[JPT][hapmap]
rs4888242	0.92[JPT][hapmap]
rs4888253	0.92[JPT][hapmap]
rs4888262	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4888265	0.81[CEU][hapmap];0.93[JPT][hapmap]
rs6564117	0.92[JPT][hapmap]
rs6564154	0.85[JPT][hapmap]
rs7185026	0.92[JPT][hapmap]
rs7189123	0.92[JPT][hapmap]
rs7194143	0.85[JPT][hapmap]
rs7204804	0.85[JPT][hapmap]
rs7205258	0.85[JPT][hapmap]
rs8058133	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8058692	0.85[JPT][hapmap]
rs8059869	0.85[JPT][hapmap]
rs918782	0.92[JPT][hapmap]
rs9923145	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9923616	0.86[JPT][hapmap]
rs9927073	0.85[JPT][hapmap]
rs9932831	0.85[JPT][hapmap]
rs9938833	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1066212	chr16:74068470-74527133	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv542954	chr16:74068470-74527133	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
5	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
6	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv833277	chr16:74334787-74498133	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv2762054	chr16:74337036-74507056	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1817585	chr16:74355081-74486997	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
11	esv1829589	chr16:74366364-74496761	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
15	nsv960357	chr16:74480805-74507776	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
18	nsv978168	chr16:74485747-74486247	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7978	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs7978	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs7978	RFWD3	cis	Whole Blood	GTEx
rs7978	RFWD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74468200-74498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:74473000-74486800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr16:74473000-74487000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr16:74475400-74486800	Weak transcription	Fetal Kidney	kidney
5	chr16:74479800-74489400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:74480000-74486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:74480000-74488200	Strong transcription	Primary T cells from cord blood	blood
8	chr16:74480400-74501000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr16:74480400-74501400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr16:74480400-74502600	Strong transcription	Thymus	Thymus
11	chr16:74480400-74530800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:74480400-74530800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:74480400-74531800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:74480600-74492800	Strong transcription	Brain Germinal Matrix	brain
15	chr16:74480600-74500200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:74480600-74503000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:74480600-74530600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:74480800-74486400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr16:74480800-74500400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:74480800-74530600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr16:74480800-74530800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:74481200-74520000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr16:74481200-74520200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr16:74481400-74487800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr16:74481600-74487000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:74481800-74487200	Strong transcription	Fetal Lung	lung
27	chr16:74481800-74487600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr16:74481800-74487600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:74481800-74492000	Strong transcription	Fetal Brain Female	brain
30	chr16:74481800-74519800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:74482000-74487600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr16:74482000-74514600	Strong transcription	Fetal Thymus	thymus
33	chr16:74482200-74487800	Strong transcription	Brain Hippocampus Middle	brain
34	chr16:74483000-74487600	Strong transcription	Primary B cells from cord blood	blood
35	chr16:74483000-74530600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr16:74483000-74530800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:74483200-74494600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:74483200-74520000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr16:74483200-74520400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr16:74483400-74492000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr16:74483600-74487600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:74483600-74487600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr16:74483800-74486600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr16:74483800-74486600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:74483800-74487400	Strong transcription	Brain Anterior Caudate	brain
46	chr16:74483800-74489000	Weak transcription	Fetal Heart	heart
47	chr16:74483800-74514400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr16:74483800-74530600	Strong transcription	Liver	Liver
49	chr16:74484000-74486800	Strong transcription	Gastric	stomach
50	chr16:74484000-74487400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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