Variant report

Variant	rs71640299
Chromosome Location	chr22:29977229-29977230
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	CREB1	chr22:29976885-29977301	A549	lung:	n/a	n/a
2	POLR2A	chr22:29976914-29977394	HepG2	liver:	n/a	n/a
3	EGR1	chr22:29976610-29977441	HCT-116	colon:	n/a	chr22:29977122-29977132 chr22:29977159-29977174 chr22:29977100-29977113 chr22:29977098-29977108 chr22:29977117-29977130 chr22:29977160-29977173 chr22:29977160-29977173 chr22:29977118-29977129 chr22:29977160-29977173 chr22:29977118-29977132 chr22:29977157-29977171
4	BCLAF1	chr22:29976888-29977336	GM12878	blood:	n/a	n/a
5	MYBL2	chr22:29975894-29977396	HepG2	liver:	n/a	n/a
6	YY1	chr22:29976838-29977245	K562	blood:	n/a	chr22:29977119-29977128 chr22:29977099-29977108 chr22:29977156-29977167 chr22:29976915-29976929 chr22:29977061-29977081
7	YY1	chr22:29976893-29977237	HCT-116	colon:	n/a	chr22:29977119-29977128 chr22:29977099-29977108 chr22:29977156-29977167 chr22:29976915-29976929 chr22:29977061-29977081
8	PML	chr22:29977012-29977297	GM12878	blood:	n/a	n/a
9	SP1	chr22:29976881-29977425	HepG2	liver:	n/a	chr22:29977097-29977109 chr22:29977098-29977107 chr22:29977159-29977168 chr22:29977121-29977133 chr22:29977099-29977108 chr22:29976890-29976899 chr22:29976889-29976901 chr22:29977097-29977108 chr22:29977122-29977131 chr22:29976891-29976900 chr22:29977098-29977108 chr22:29977098-29977112 chr22:29977121-29977133 chr22:29977098-29977108 chr22:29976890-29976904 chr22:29977098-29977107 chr22:29977097-29977109 chr22:29976890-29976900 chr22:29977123-29977132 chr22:29976889-29976901
10	ELF1	chr22:29976963-29977398	K562	blood:	n/a	chr22:29977120-29977132 chr22:29977119-29977128
11	POU2F2	chr22:29976960-29977404	GM12891	blood:	n/a	n/a
12	POLR2A	chr22:29976890-29977397	GM12892	blood:	n/a	n/a
13	FOXP2	chr22:29977021-29977383	SK-N-MC	brain:	n/a	n/a
14	RCOR1	chr22:29977037-29977368	Hela-S3	cervix:	n/a	n/a
15	USF2	chr22:29977080-29977340	Hela-S3	cervix:	n/a	n/a
16	ELF1	chr22:29977001-29977339	HepG2	liver:	n/a	chr22:29977120-29977132 chr22:29977119-29977128
17	TBP	chr22:29975884-29977282	HepG2	liver:	n/a	n/a
18	POLR2A	chr22:29976821-29977322	GM12878	blood:	n/a	n/a
19	ZMIZ1	chr22:29977050-29977237	K562	blood:	n/a	n/a
20	USF1	chr22:29977031-29977291	GM12878	blood:	n/a	chr22:29977178-29977189
21	POLR2A	chr22:29976772-29977395	ECC-1	luminal epithelium:	n/a	n/a
22	CREB1	chr22:29975752-29977426	HepG2	liver:	n/a	n/a
23	MAX	chr22:29976972-29977235	HepG2	liver:	n/a	chr22:29977160-29977170
24	ZEB1	chr22:29976787-29977355	GM12878	blood:	n/a	n/a
25	SP1	chr22:29976621-29977503	H1-hESC	embryonic stem cell:	n/a	chr22:29977097-29977109 chr22:29976850-29976864 chr22:29977098-29977107 chr22:29977159-29977168 chr22:29977121-29977133 chr22:29977099-29977108 chr22:29976890-29976899 chr22:29976889-29976901 chr22:29977097-29977108 chr22:29977122-29977131 chr22:29976891-29976900 chr22:29977098-29977108 chr22:29977098-29977112 chr22:29977121-29977133 chr22:29977098-29977108 chr22:29976850-29976859 chr22:29976890-29976904 chr22:29977098-29977107 chr22:29977097-29977109 chr22:29976821-29976835 chr22:29976890-29976900 chr22:29977123-29977132 chr22:29976889-29976901
26	TAF1	chr22:29976912-29977363	GM12891	blood:	n/a	n/a
27	EGR1	chr22:29976892-29977354	ECC-1	luminal epithelium:	n/a	chr22:29977122-29977132 chr22:29977159-29977174 chr22:29977100-29977113 chr22:29977098-29977108 chr22:29977117-29977130 chr22:29977160-29977173 chr22:29977160-29977173 chr22:29977118-29977129 chr22:29977160-29977173 chr22:29977118-29977132 chr22:29977157-29977171
28	POLR2A	chr22:29976791-29977341	PANC-1	pancreas:	n/a	n/a
29	SP1	chr22:29976871-29977416	H1-hESC	embryonic stem cell:	n/a	chr22:29977097-29977109 chr22:29977098-29977107 chr22:29977159-29977168 chr22:29977121-29977133 chr22:29977099-29977108 chr22:29976890-29976899 chr22:29976889-29976901 chr22:29977097-29977108 chr22:29977122-29977131 chr22:29976891-29976900 chr22:29977098-29977108 chr22:29977098-29977112 chr22:29977121-29977133 chr22:29977098-29977108 chr22:29976890-29976904 chr22:29977098-29977107 chr22:29977097-29977109 chr22:29976890-29976900 chr22:29977123-29977132 chr22:29976889-29976901
30	HNF4A	chr22:29976024-29977381	HepG2	liver:	n/a	chr22:29976393-29976408
31	RCOR1	chr22:29975851-29977344	HepG2	liver:	n/a	n/a
32	POLR2A	chr22:29976944-29977370	GM12878	blood:	n/a	n/a
33	POLR2A	chr22:29976773-29977391	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr22:29976869-29977335	GM12891	blood:	n/a	n/a
35	ELF1	chr22:29976815-29977361	MCF-7	breast:	n/a	chr22:29977120-29977132 chr22:29977119-29977128
36	TAF1	chr22:29976628-29977289	HepG2	liver:	n/a	n/a
37	MAX	chr22:29976719-29977435	A549	lung:	n/a	chr22:29977160-29977170
38	TAF1	chr22:29976905-29977309	SK-N-SH	brain:	n/a	n/a
39	TAF1	chr22:29976790-29977307	A549	lung:	n/a	n/a
40	TCF12	chr22:29976507-29977411	A549	lung:	n/a	n/a
41	HEY1	chr22:29975717-29977479	HepG2	liver:	n/a	n/a
42	TBL1XR1	chr22:29977080-29977254	K562	blood:	n/a	n/a
43	RFX5	chr22:29976974-29977332	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr22:29976819-29977511	Hela-S3	cervix:	n/a	n/a
45	JUND	chr22:29977006-29977333	K562	blood:	n/a	chr22:29977167-29977178
46	POLR2A	chr22:29975710-29977396	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr22:29976836-29977392	HCT-116	colon:	n/a	n/a
48	SIN3A	chr22:29976267-29977266	H1-hESC	embryonic stem cell:	n/a	chr22:29976271-29976284
49	TAF1	chr22:29976858-29977340	PFSK-1	brain:	n/a	n/a
50	NFIC	chr22:29976957-29977431	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:29977228-29977278	MCF10A-Er-Src	breast:	n/a
2	chr22:29977228-29977278	AG04449	skin:	fetal
3	chr22:29977228-29977278	ovcar-3	ovarian:	n/a
4	chr22:29977228-29977278	ProgFib	skin:	n/a
5	chr22:29977203-29977253	RPTEC	kidney:	n/a
6	chr22:29977203-29977253	MCF10A-Er-Src	breast:	n/a
7	chr22:29977203-29977253	HL-60	blood:	n/a
8	chr22:29977203-29977253	HUVEC	blood vessel:	n/a
9	chr22:29977203-29977253	BE2_C	brain:	n/a
10	chr22:29977203-29977253	Hela-S3	cervix:	n/a
11	chr22:29977228-29977278	NHBE	bronchial:	n/a
12	chr22:29977203-29977253	SK-N-SH	brain:	n/a
13	chr22:29977228-29977278	GM12878	blood:	n/a
14	chr22:29977228-29977278	NT2-D1	testis:	n/a
15	chr22:29977203-29977253	NT2-D1	testis:	n/a
16	chr22:29977203-29977253	HRE	kidney:	n/a
17	chr22:29977228-29977278	HMEC	breast:	n/a
18	chr22:29977228-29977278	GM12891	blood:	n/a
19	chr22:29977228-29977278	NB4	blood:	n/a
20	chr22:29977228-29977278	T-47D	breast:	n/a
21	chr22:29977203-29977253	NH-A	brain:	n/a
22	chr22:29977228-29977278	U87	brain:	n/a
23	chr22:29977203-29977253	AG04450	lung:	fetal
24	chr22:29977203-29977253	K562	blood:	n/a
25	chr22:29977203-29977253	HRPEpiC	eye:	n/a
26	chr22:29977228-29977278	NH-A	brain:	n/a
27	chr22:29977228-29977278	BJ	skin:	n/a
28	chr22:29977228-29977278	PFSK-1	brain:	n/a
29	chr22:29977228-29977278	HCPEpiC	choroid plexus:	n/a
30	chr22:29977203-29977253	PrEC	prostate:	n/a
31	chr22:29977203-29977253	HCM	heart:	n/a
32	chr22:29977228-29977278	AG10803	skin:	n/a
33	chr22:29977203-29977253	AG09319	gingival:	n/a
34	chr22:29977228-29977278	Caco-2	colon:	n/a
35	chr22:29977228-29977278	SAEC	small airway:	n/a
36	chr22:29977203-29977253	A549	lung:	n/a
37	chr22:29977203-29977253	SK-N-SH_RA	brain:	n/a
38	chr22:29977228-29977278	AG04450	lung:	fetal
39	chr22:29977228-29977278	AG09319	gingival:	n/a
40	chr22:29977203-29977253	CMK	blood:	n/a
41	chr22:29977203-29977253	GM12892	blood:	n/a
42	chr22:29977203-29977253	SKMC	muscle:	n/a
43	chr22:29977228-29977278	IMR90	lung:	fetal
44	chr22:29977228-29977278	PANC-1	pancreas:	n/a
45	chr22:29977203-29977253	GM12891	blood:	n/a
46	chr22:29977228-29977278	BE2_C	brain:	n/a
47	chr22:29977228-29977278	HL-60	blood:	n/a
48	chr22:29977203-29977253	AG04449	skin:	fetal
49	chr22:29977203-29977253	AoSMC	blood vessel:	n/a
50	chr22:29977203-29977253	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29975483..29978642-chr22:29996311..30000725,6	MCF-7	breast:
2	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:
3	chr22:29663275..29666008-chr22:29976454..29978804,2	K562	blood:
4	chr22:29948374..29951089-chr22:29975785..29978624,4	MCF-7	breast:
5	chr22:29782601..29785697-chr22:29975164..29978533,5	MCF-7	breast:
6	chr22:29975560..29978145-chr22:29998416..30001350,4	MCF-7	breast:
7	chr22:29948193..29950224-chr22:29975940..29978547,6	MCF-7	breast:

Variant related genes	Relation type
NIPSNAP1	TF binding region
NIPSNAP1	CpG island
ENSG00000186575	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000100296	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2009354	0.87[AFR][1000 genomes]
rs55797751	1.00[ASN][1000 genomes]
rs56188151	0.87[AFR][1000 genomes]
rs57986874	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv521852	chr22:29974831-29983138	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71640299	ENSG00000184117	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29975800-29977800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr22:29976000-29977400	Active TSS	NHLF	lung
3	chr22:29976000-29977800	Active TSS	Primary T cells from cord blood	blood
4	chr22:29976000-29977800	Active TSS	Fetal Kidney	kidney
5	chr22:29976200-29977400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr22:29976200-29977400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr22:29976200-29977600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:29976200-29977600	Active TSS	K562	blood
9	chr22:29976200-29977800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr22:29976200-29977800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:29976200-29978000	Active TSS	Rectal Smooth Muscle	rectum
12	chr22:29976400-29977400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr22:29976400-29977400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr22:29976400-29977400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29976400-29977400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr22:29976400-29977400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:29976400-29977400	Active TSS	HSMMtube	muscle
18	chr22:29976400-29977600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr22:29976400-29977600	Active TSS	Fetal Lung	lung
20	chr22:29976400-29977800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr22:29976400-29977800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr22:29976400-29977800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr22:29976400-29977800	Active TSS	Brain Anterior Caudate	brain
24	chr22:29976400-29977800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr22:29976600-29977400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr22:29976600-29977400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr22:29976600-29977400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr22:29976600-29977400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:29976600-29977400	Active TSS	Aorta	Aorta
30	chr22:29976600-29977400	Active TSS	Fetal Brain Male	brain
31	chr22:29976600-29977400	Active TSS	Ovary	ovary
32	chr22:29976600-29977400	Active TSS	Placenta Amnion	Placenta Amnion
33	chr22:29976600-29977400	Active TSS	Psoas Muscle	Psoas
34	chr22:29976600-29977400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr22:29976600-29977400	Active TSS	Stomach Mucosa	stomach
36	chr22:29976600-29977400	Active TSS	HMEC	breast
37	chr22:29976600-29977600	Active TSS	H1 Cell Line	embryonic stem cell
38	chr22:29976600-29977600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr22:29976600-29977600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr22:29976600-29977600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:29976600-29977600	Active TSS	Fetal Intestine Large	intestine
42	chr22:29976600-29977600	Active TSS	Hela-S3	cervix
43	chr22:29976600-29977600	Active TSS	NH-A	brain
44	chr22:29976600-29977600	Active TSS	NHDF-Ad	bronchial
45	chr22:29976600-29977800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr22:29976600-29977800	Active TSS	Brain Substantia Nigra	brain
47	chr22:29976600-29978000	Active TSS	A549	lung
48	chr22:29976800-29977400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr22:29976800-29977400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:29976800-29977400	Active TSS	Primary neutrophils fromperipheralblood	blood

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