Variant report

Variant	rs12228207
Chromosome Location	chr12:104196734-104196735
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	JUND	chr12:104195702-104196765	SK-N-SH	brain:	n/a	n/a
2	RXRA	chr12:104195911-104196776	SK-N-SH	brain:	n/a	chr12:104196601-104196610
3	TCF12	chr12:104195446-104196953	SK-N-SH	brain:	n/a	chr12:104195531-104195541
4	EP300	chr12:104195870-104196754	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr12:104195652-104196878	SK-N-SH	brain:	n/a	n/a
6	EP300	chr12:104195482-104196842	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr12:104195747-104196756	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr12:104195797-104196885	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:104195626-104196966	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
2	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
3	chr12:104196315..104200600-chr12:104233023..104235965,5	MCF-7	breast:
4	chr12:104163207..104165311-chr12:104196733..104198239,2	K562	blood:
5	chr12:104190724..104195360-chr12:104196501..104199658,6	MCF-7	breast:

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10861095	0.89[JPT][hapmap]
rs10861096	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10861097	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10861104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861105	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861109	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111762	0.80[ASN][1000 genomes]
rs11111763	0.80[ASN][1000 genomes]
rs11111767	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11111771	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11111778	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111786	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111788	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111789	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11111793	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111795	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11111796	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111799	0.92[ASN][1000 genomes]
rs11610714	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12229276	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12830701	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1866292	0.82[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs1866295	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2033774	0.86[AFR][1000 genomes]
rs34307072	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35371470	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35746861	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35945096	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36034617	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3751204	0.88[JPT][hapmap]
rs3812803	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3812805	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3935416	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964289	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964298	0.80[ASN][1000 genomes]
rs4964623	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964780	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964794	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4964805	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964806	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964812	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964823	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4964827	0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs4964830	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs67825151	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7134701	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs751448	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs869993	0.89[JPT][hapmap]
rs9132	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs954920	0.89[JPT][hapmap]

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	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12228207	RP11-341G23.4	cis	Thyroid	GTEx
rs12228207	RP11-341G23.4	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:104185800-104198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:104187800-104198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
11	chr12:104190800-104198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:104190800-104201800	Weak transcription	Gastric	stomach
13	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:104192000-104200400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:104192800-104197000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:104192800-104199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:104193000-104196800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:104193400-104197000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:104193400-104197000	Enhancers	Fetal Muscle Leg	muscle
24	chr12:104193600-104196800	Enhancers	HepG2	liver
25	chr12:104193600-104196800	Enhancers	HSMM	muscle
26	chr12:104193600-104204000	Weak transcription	Primary T cells from cord blood	blood
27	chr12:104193800-104198200	Genic enhancers	K562	blood
28	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:104194400-104197000	Enhancers	NH-A	brain
30	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:104194600-104196800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:104194600-104196800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr12:104194600-104197000	Enhancers	Psoas Muscle	Psoas
34	chr12:104194600-104197200	Enhancers	Osteobl	bone
35	chr12:104194600-104197600	Enhancers	Rectal Smooth Muscle	rectum
36	chr12:104194600-104198800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:104194600-104199400	Weak transcription	Esophagus	oesophagus
38	chr12:104194600-104199600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:104194600-104199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:104194600-104203800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:104194800-104196800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
46	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:104195000-104196800	Enhancers	Hela-S3	cervix
48	chr12:104195000-104197000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr12:104195000-104198000	Weak transcription	NHDF-Ad	bronchial
50	chr12:104195000-104198400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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