Variant report

Variant	rs1136774
Chromosome Location	chr1:150738197-150738198
allele	A/G
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	IRF4	chr1:150738082-150738546	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:150738080-150738243	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:150737927-150738563	GM12878	blood:	n/a	n/a
4	TAF1	chr1:150738049-150738425	GM12891	blood:	n/a	n/a
5	MYC	chr1:150738120-150738503	NB4	blood:	n/a	chr1:150738292-150738301
6	EP300	chr1:150737980-150738498	GM12878	blood:	n/a	chr1:150738310-150738324 chr1:150738330-150738344
7	SPI1	chr1:150737720-150738753	GM12878	blood:	n/a	chr1:150738311-150738320 chr1:150738308-150738321 chr1:150738309-150738322
8	SPI1	chr1:150737929-150738561	GM12891	blood:	n/a	chr1:150738311-150738320 chr1:150738308-150738321 chr1:150738309-150738322
9	PML	chr1:150737853-150738424	K562	blood:	n/a	n/a
10	MEF2A	chr1:150737908-150738424	GM12878	blood:	n/a	chr1:150738028-150738037 chr1:150738021-150738042 chr1:150738027-150738038 chr1:150738021-150738042 chr1:150738025-150738040 chr1:150738026-150738040
11	SPI1	chr1:150737631-150738761	HL-60	blood:	n/a	chr1:150738311-150738320 chr1:150738308-150738321 chr1:150738309-150738322
12	POLR2A	chr1:150737997-150738567	GM12891	blood:	n/a	n/a
13	POLR2A	chr1:150738030-150738357	GM12878	blood:	n/a	n/a
14	STAT3	chr1:150737899-150738606	GM12878	blood:	n/a	n/a
15	EP300	chr1:150737996-150738507	GM12878	blood:	n/a	chr1:150738310-150738324 chr1:150738330-150738344
16	CHD1	chr1:150737238-150738349	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:150738039-150738445	GM12878	blood:	n/a	n/a
18	TAF1	chr1:150738016-150738319	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:150738196-150738566	K562	blood:	n/a	n/a
20	MYC	chr1:150738011-150738437	K562	blood:	n/a	chr1:150738292-150738301
21	TCF12	chr1:150737585-150738303	SK-N-SH	brain:	n/a	n/a
22	BCLAF1	chr1:150737934-150738532	GM12878	blood:	n/a	chr1:150738330-150738339
23	USF2	chr1:150738032-150738474	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:150737952-150738444	GM12892	blood:	n/a	n/a
25	ATF2	chr1:150737922-150738587	GM12878	blood:	n/a	n/a
26	PML	chr1:150737980-150738396	GM12878	blood:	n/a	n/a
27	MXI1	chr1:150737692-150738467	GM12878	blood:	n/a	n/a
28	BHLHE40	chr1:150738026-150738513	GM12878	blood:	n/a	n/a
29	BCL3	chr1:150738007-150738423	GM12878	blood:	n/a	chr1:150738330-150738339
30	POLR2A	chr1:150737997-150738463	GM18505	blood:	n/a	n/a
31	RELA	chr1:150738065-150738480	GM19099	blood:	n/a	n/a
32	POLR2A	chr1:150737896-150738560	GM12892	blood:	n/a	n/a
33	TCF7L2	chr1:150737710-150738266	HepG2	liver:	n/a	chr1:150738154-150738168
34	SPI1	chr1:150737941-150738492	HL-60	blood:	n/a	chr1:150738311-150738320 chr1:150738308-150738321 chr1:150738309-150738322
35	USF1	chr1:150738189-150738366	K562	blood:	n/a	n/a
36	POLR2A	chr1:150737709-150738309	SK-N-MC	brain:	n/a	n/a
37	CUX1	chr1:150737845-150738567	K562	blood:	n/a	n/a
38	PAX5	chr1:150737882-150738360	GM12891	blood:	n/a	chr1:150738330-150738339
39	REST	chr1:150737995-150738562	HL-60	blood:	n/a	n/a
40	POLR2A	chr1:150737985-150738649	U87	brain:	n/a	n/a
41	RCOR1	chr1:150738124-150738404	K562	blood:	n/a	n/a
42	EBF1	chr1:150737981-150738491	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:150738025-150738522	GM12878	blood:	n/a	n/a
44	RUNX3	chr1:150737886-150738514	GM12878	blood:	n/a	n/a
45	IRF1	chr1:150738013-150738501	K562	blood:	n/a	chr1:150738275-150738289 chr1:150738332-150738346 chr1:150738314-150738323 chr1:150738329-150738343 chr1:150738327-150738347 chr1:150738329-150738339
46	REST	chr1:150738080-150738480	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr1:150737944-150738415	GM12892	blood:	n/a	n/a
48	IRF1	chr1:150737923-150738560	K562	blood:	n/a	chr1:150738275-150738289 chr1:150738332-150738346 chr1:150738314-150738323 chr1:150738329-150738343 chr1:150738327-150738347 chr1:150738329-150738339
49	CREB1	chr1:150737954-150738573	GM12878	blood:	n/a	n/a
50	RCOR1	chr1:150738033-150738461	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:150738173-150738223	GM19239	blood:	n/a
2	chr1:150738173-150738223	GM12891	blood:	n/a
3	chr1:150738173-150738223	A549	lung:	n/a
4	chr1:150738173-150738223	SKMC	muscle:	n/a
5	chr1:150738173-150738223	PFSK-1	brain:	n/a
6	chr1:150738173-150738223	CMK	blood:	n/a
7	chr1:150738173-150738223	NT2-D1	testis:	n/a
8	chr1:150738173-150738223	AG09319	gingival:	n/a
9	chr1:150738173-150738223	SAEC	small airway:	n/a
10	chr1:150738173-150738223	HPAEpiC	pulmonary alveolar:	n/a
11	chr1:150738173-150738223	AoSMC	blood vessel:	n/a
12	chr1:150738173-150738223	AG04450	lung:	fetal
13	chr1:150738173-150738223	H1-hESC	embryonic stem cell:	embryo
14	chr1:150738173-150738223	HMEC	breast:	n/a
15	chr1:150738173-150738223	HRE	kidney:	n/a
16	chr1:150738173-150738223	GM12892	blood:	n/a
17	chr1:150738173-150738223	NHDF-neo	bronchial:	n/a
18	chr1:150738173-150738223	ovcar-3	ovarian:	n/a
19	chr1:150738173-150738223	HRCEpiC	kidney:	n/a
20	chr1:150738173-150738223	GM12878	blood:	n/a
21	chr1:150738173-150738223	MCF10A-Er-Src	breast:	n/a
22	chr1:150738173-150738223	HUVEC	blood vessel:	n/a
23	chr1:150738173-150738223	LNCaP	prostate:	n/a
24	chr1:150738173-150738223	HEK293	kidney:	embryo
25	chr1:150738173-150738223	AG04449	skin:	fetal
26	chr1:150738173-150738223	NH-A	brain:	n/a
27	chr1:150738173-150738223	Hepatocyte	liver:	n/a
28	chr1:150738173-150738223	T-47D	breast:	n/a
29	chr1:150738173-150738223	Caco-2	colon:	n/a
30	chr1:150738173-150738223	SK-N-SH	brain:	n/a
31	chr1:150738173-150738223	ProgFib	skin:	n/a
32	chr1:150738173-150738223	BE2_C	brain:	n/a
33	chr1:150738173-150738223	HCPEpiC	choroid plexus:	n/a
34	chr1:150738173-150738223	RPTEC	kidney:	n/a
35	chr1:150738173-150738223	ECC-1	luminal epithelium:	n/a
36	chr1:150738173-150738223	PANC-1	pancreas:	n/a
37	chr1:150738173-150738223	SK-N-MC	brain:	n/a
38	chr1:150738173-150738223	HL-60	blood:	n/a
39	chr1:150738173-150738223	HNPCEpiC	eye:	n/a
40	chr1:150738173-150738223	IMR90	lung:	fetal
41	chr1:150738173-150738223	U87	brain:	n/a
42	chr1:150738173-150738223	NHBE	bronchial:	n/a
43	chr1:150738173-150738223	K562	blood:	n/a
44	chr1:150738173-150738223	HCT-116	colon:	n/a
45	chr1:150738173-150738223	NB4	blood:	n/a
46	chr1:150738173-150738223	HCF	heart:	n/a
47	chr1:150738173-150738223	BJ	skin:	n/a
48	chr1:150738173-150738223	HAEpiC	amniotic membrane:	n/a
49	chr1:150738173-150738223	MCF-7	breast:	n/a
50	chr1:150738173-150738223	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150550688..150552369-chr1:150735871..150738707,2	MCF-7	breast:

Variant related genes	Relation type
CTSS	TF binding region
CTSS	CpG island
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1081512	0.80[EUR][1000 genomes]
rs10888388	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11204693	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs11204695	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11204702	0.83[AFR][1000 genomes]
rs11204712	0.82[ASN][1000 genomes]
rs11204725	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs11204737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs12125650	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126004	0.80[EUR][1000 genomes]
rs12130363	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12403609	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12410050	0.80[EUR][1000 genomes]
rs12568757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12725806	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12758227	0.84[EUR][1000 genomes]
rs16841689	0.82[YRI][hapmap]
rs17599629	0.91[YRI][hapmap]
rs2039590	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2089081	0.87[EUR][1000 genomes]
rs34002273	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486836	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4970924	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs4970926	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs4970976	0.84[EUR][1000 genomes]
rs6587520	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6694531	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7520022	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs7534124	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9733	0.89[CEU][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv872419	chr1:150699199-150738759	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1008381	chr1:150721254-150745558	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1136774	ARNT	cis	normal skin	skin_eQTL
rs1136774	ARNT	cis	multi-tissue	Pritchard
rs1136774	HORMAD1	cis	lesional skin	skin_eQTL
rs1136774	ARNT	cis	uninvolved skin	skin_eQTL
rs1136774	CTSK	cis	multi-tissue	Pritchard
rs1136774	ARNT	cis	lesional skin	skin_eQTL
rs1136774	HORMAD1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150734800-150738400	Active TSS	GM12878-XiMat	blood
2	chr1:150735600-150738600	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:150736200-150738400	Active TSS	Brain Anterior Caudate	brain
4	chr1:150736200-150738600	Active TSS	Colonic Mucosa	Colon
5	chr1:150736400-150738200	Active TSS	Brain Hippocampus Middle	brain
6	chr1:150736400-150738200	Enhancers	NH-A	brain
7	chr1:150736400-150738600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr1:150736600-150738400	Active TSS	Duodenum Mucosa	Duodenum
9	chr1:150736600-150738400	Active TSS	Right Atrium	heart
10	chr1:150737000-150738200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:150737000-150738200	Enhancers	HSMM	muscle
12	chr1:150737000-150738400	Active TSS	Fetal Intestine Large	intestine
13	chr1:150737000-150738400	Active TSS	Stomach Mucosa	stomach
14	chr1:150737000-150738400	Active TSS	Stomach Smooth Muscle	stomach
15	chr1:150737000-150738400	Active TSS	Thymus	Thymus
16	chr1:150737000-150738400	Enhancers	HSMMtube	muscle
17	chr1:150737200-150738200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:150737200-150738200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:150737200-150738400	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr1:150737200-150738600	Flanking Active TSS	A549	lung
21	chr1:150737200-150761800	Weak transcription	Spleen	Spleen
22	chr1:150737400-150738200	Active TSS	Placenta	Placenta
23	chr1:150737400-150738200	Active TSS	K562	blood
24	chr1:150737400-150738400	Active TSS	Primary monocytes fromperipheralblood	blood
25	chr1:150737400-150738400	Active TSS	Primary B cells from peripheral blood	blood
26	chr1:150737400-150738400	Active TSS	Primary T cells fromperipheralblood	blood
27	chr1:150737400-150738400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:150737400-150738400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:150737400-150738400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:150737400-150738400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:150737400-150738400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:150737400-150738400	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:150737400-150738400	Active TSS	Liver	Liver
34	chr1:150737400-150738400	Active TSS	Fetal Muscle Leg	muscle
35	chr1:150737400-150738400	Active TSS	Fetal Thymus	thymus
36	chr1:150737400-150738400	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:150737400-150738400	Enhancers	Hela-S3	cervix
38	chr1:150737400-150738600	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:150737400-150738600	Active TSS	Adipose Nuclei	Adipose
40	chr1:150737400-150738800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:150737400-150740000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:150737600-150738200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:150737600-150738200	Flanking Active TSS	HUVEC	blood vessel
44	chr1:150737600-150738200	Active TSS	NHLF	lung
45	chr1:150737600-150738400	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:150737600-150738400	Active TSS	Fetal Lung	lung
47	chr1:150737600-150738400	Active TSS	Fetal Stomach	stomach
48	chr1:150737600-150738400	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr1:150737600-150738600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr1:150737600-150738600	Active TSS	Colon Smooth Muscle	Colon

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