Variant report

Variant	rs6678672
Chromosome Location	chr1:151955009-151955010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151953443..151955255-chr1:151956966..151958733,2	K562	blood:
2	chr1:151906693..151908513-chr1:151954832..151956959,2	K562	blood:
3	chr1:151861526..151864344-chr1:151954395..151956791,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038747	0.89[CHB][hapmap]
rs10494270	0.85[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11204906	0.82[AMR][1000 genomes]
rs11204919	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204920	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204922	0.90[CHB][hapmap]
rs11582739	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12083193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095483	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12116923	0.81[CHB][hapmap]
rs12239945	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1387833	0.82[CHB][hapmap]
rs1532133	0.86[CHB][hapmap]
rs16833668	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16833669	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16833670	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16833728	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16833743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844543	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1979637	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2012674	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279501	0.86[CHB][hapmap]
rs2279502	0.86[CHB][hapmap]
rs2337685	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2337686	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2338019	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs2338206	0.82[AMR][1000 genomes]
rs2932570	0.86[CHB][hapmap]
rs2932579	0.82[CHB][hapmap]
rs2932580	0.91[ASN][1000 genomes]
rs2932590	0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap]
rs2999526	0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs2999528	0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs2999531	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs2999534	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs2999539	0.81[CHB][hapmap];0.87[TSI][hapmap]
rs3007708	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs34251437	0.81[ASN][1000 genomes]
rs3791153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845719	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56000812	0.87[AMR][1000 genomes]
rs56078223	0.87[AMR][1000 genomes]
rs56170235	0.82[AMR][1000 genomes]
rs56313205	0.83[AMR][1000 genomes]
rs57674198	0.82[AMR][1000 genomes]
rs57785325	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61814883	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61814891	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817695	0.82[AMR][1000 genomes]
rs61817697	0.82[AMR][1000 genomes]
rs61817719	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61817720	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61817722	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817723	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61817724	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61817725	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6587632	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6587633	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6587634	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6587635	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587636	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587637	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587638	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587643	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587644	0.86[EUR][1000 genomes]
rs6657658	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6659662	0.82[AMR][1000 genomes]
rs6662602	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6662611	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6662728	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6663064	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6672064	0.82[AMR][1000 genomes]
rs6675930	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6677973	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6682605	0.87[ASN][1000 genomes]
rs6684114	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6684312	0.86[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs6686874	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690449	0.84[AMR][1000 genomes]
rs6691212	0.81[ASN][1000 genomes]
rs6693388	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6693396	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6693901	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6695324	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6701374	0.87[AMR][1000 genomes]
rs6703448	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6703465	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72694840	0.84[AMR][1000 genomes]
rs7535002	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538652	0.86[ASN][1000 genomes]
rs7541099	0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7554832	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7554859	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs902313	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs971887	0.95[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9943221	0.86[CHB][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9943251	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6678672	THEM4	cis	cerebellum	SCAN
rs6678672	S100A10	cis	cerebellum	SCAN
rs6678672	LCE2C	cis	cerebellum	SCAN
rs6678672	NBPF18P	cis	Nerve Tibial	GTEx
rs6678672	THEM4	cis	lymphoblastoid	seeQTL
rs6678672	S100A10	cis	parietal	SCAN
rs6678672	S100A10	cis	multi-tissue	Pritchard
rs6678672	THEM4	cis	parietal	SCAN
rs6678672	ADAMTSL4	cis	cerebellum	SCAN
rs6678672	S100A10	cis	lymphoblastoid	seeQTL
rs6678672	SLC25A40	trans	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
4	chr1:151946200-151956200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:151946600-151957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:151946600-151958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:151948000-151956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:151948400-151955200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:151949200-151963200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:151949800-151957200	Weak transcription	Stomach Mucosa	stomach
11	chr1:151950000-151956600	Genic enhancers	A549	lung
12	chr1:151951000-151961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:151951600-151960800	Weak transcription	Fetal Thymus	thymus
14	chr1:151951800-151961800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:151952400-151959600	Genic enhancers	NHDF-Ad	bronchial
16	chr1:151952400-151960800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:151952600-151957800	Genic enhancers	Fetal Intestine Small	intestine
18	chr1:151952600-151960400	Genic enhancers	NHEK	skin
19	chr1:151952800-151955400	Genic enhancers	HMEC	breast
20	chr1:151952800-151956200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:151952800-151956200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:151952800-151956400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:151952800-151957200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:151952800-151957400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:151952800-151959400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:151953000-151956200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:151953000-151956400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:151953000-151956600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:151953000-151956600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:151953000-151957200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:151953000-151958400	Strong transcription	Lung	lung
32	chr1:151953000-151958400	Strong transcription	Spleen	Spleen
33	chr1:151953000-151958600	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:151953000-151958800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:151953200-151956200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:151953200-151956200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:151953200-151956400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:151953200-151957000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:151953200-151958800	Strong transcription	Fetal Lung	lung
40	chr1:151953400-151956200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:151953400-151956400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:151953400-151956800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:151953400-151958600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:151953400-151958600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:151953400-151958600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:151953400-151958800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr1:151953400-151959200	Genic enhancers	Placenta Amnion	Placenta Amnion
48	chr1:151953400-151959200	Strong transcription	Dnd41	blood
49	chr1:151953400-151959400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:151953400-151959400	Strong transcription	Psoas Muscle	Psoas

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